SNP pipeline analysis of subjects with 3 body site results

library(tidyverse)
source("MAP_functions.R")

Subject 26

SNP_analysis_pipeline(subject_id = 26)

[1] "SUBJECT_ID is 26"
[1] "Rare iSNP cutoff =  3"
[1] "num rare iSNPs =  4383"
[1] "num common iSNPs =  4970"
[1] "Recombination block cutoff = 3"
[1] "Num bases in C recomb blocks=  24514"
[1] "Num bases in R recomb = blocks 24514"
[1] "Num bases in V recomb = blocks 3567"
[1] "Coverage cutoff =  10"
[1] "Numbers of R bases above cutoff is  1036306"
[1] "Numbers of C bases above cutoff is  1036204"
[1] "Numbers of V bases above cutoff is  1035660"
[1] "Number of iSNP positions =  5311"
[1] "R only fixed SNPs (RonlyF) =  0"
[1] "R only rare fixed SNPs (RonlyFrare) =  0"
[1] "R only fixed SNPs in recombinant regions (RonlyFrecomb) =  0"
[1] "R only iSNPs (RonlyRI) =  36"
[1] "R only rare iSNPs (RonlyRIrare) =  16"
[1] "R only iSNPs in recombinant regions (RonlyRIrecomb) =  0"
[1] "C only fixed SNPs (ConlyF) =  0"
[1] "C only rare fixed SNPs (ConlyFrare) =  0"
[1] "C only fixed SNPs in recombinant regions (ConlyFrecomb) =  0"
[1] "C only iSNPs (ConlyRI) =  4"
[1] "C only rare iSNPs (ConlyRIrare) =  0"
[1] "C only iSNPs in recombinant regions (ConlyRIrecomb) =  0"
[1] "V only fixed SNPs (VonlyF) =  0"
[1] "V only rare fixed SNPs (VonlyFrare) =  0"
[1] "V only fixed SNPs in recombinant regions (VonlyFrecombb) =  0"
[1] "V only iSNPs (VonlyRI) =  0"
[1] "V only rare iSNPs (VonlyRIrare) =  0"
[1] "V only iSNPs in recombinant regions (VonlyRIrecomb) =  0"
[1] "RC only fixed SNPs (RConlyF) =  0"
[1] "RC only rare fixed SNPs (RConlyFrare) =  0"
[1] "RC only fixed SNPs in recombinant regions (RConlyFrecomb) =  0"
[1] "RC only iSNPs (RConlyRI) =  6"
[1] "RC only rare iSNPs (RConlyRIrare) =  0"
[1] "RC only iSNPs in recombinant regions (RConlyRIrecomb) =  0"
[1] "RV only fixed SNPs (RVonlyF) =  0"
[1] "RV only rare fixed SNPs (RVonlyFrare) =  0"
[1] "RV only fixed SNPs in recombinant regions (RVonlyFrecomb) =  0"
[1] "RV only iSNPs (RVonlyRI) =  0"
[1] "RV only rare iSNPs (RVonlyRIrare) =  0"
[1] "RV only iSNPs in recombinant regions (RVonlyRIrecomb) =  0"
[1] "VC only fixed SNPs (VConlyF) =  0"
[1] "VC only rare fixed SNPs (VConlyFrare) =  0"
[1] "VC only fixed SNPs in recombinant regions (VConlyFrecomb) =  0"
[1] "VC only iSNPs (VConlyRI) =  2"
[1] "VC only rare iSNPs (VConlyRIrare) =  1"
[1] "VC only iSNPs in recombinant regions (VConlyRIrecomb) =  0"
[1] "All fixed SNPs (AllF) =  5229"
[1] "All rare fixed SNPs (AllFrare) =  1179"
[1] "All fixed SNPs in recombinant regions (AllFrecomb) =  12"
[1] "All iSNPs (AllRI) =  16"
[1] "All rare  iSNPs (AllRIrare) =  0"
[1] "All iSNPs in recombinant regions (AllRIrecomb) =  0"
[1] "R is fixed, V only is intermediate, and rare (RonlyF_VIrare) =  0"
[1] "R is fixed, C only is intermediate, and rare (RonlyF_CIrare) =  0"
[1] "R is fixed, V and C are intermediate, and rare (RonlyF_CandVIrare) =  0"
[1] "C is fixed, V only is intermediate, and rare (ConlyF_VIrare) =  0"
[1] "C is fixed, R only is intermediate, and rare (ConlyF_RIrare) =  0"
[1] "C is fixed, R and V are intermediate, and rare (ConlyF_RandVIrare) =  0"
[1] "V is fixed, C only is intermediate, and rare (VonlyF_CIrare) =  0"
[1] "V is fixed, R only is intermediate, and rare (VonlyF_RIrare) =  0"
[1] "V is fixed, R and C are intermediate, and rare (VonlyF_CandRIrare) =  0"
[1] "R and C are fixed, V is intermediate, and rare (RCF_VIrare) =  1"
[1] "R and V are fixed, C is intermediate, and rare (RVF_CIrare) =  0"
[1] "V and C are fixed, R is intermediate, and rare (CVF_RIrare) =  1"

Warning: Removed 7 rows containing missing values (geom_point).
Warning: Removed 8 rows containing missing values (geom_point).
Warning: Removed 3 rows containing missing values (geom_point).
Warning: Removed 18 rows containing non-finite values (stat_boxplot).

[1] "Number cDenovo Ref SNPs for C =  334"
[1] "Number cDenovo Non-Ref SNPs for C =  1528"
[1] "Number cDenovo iSNPs for C =  1"
[1] "Number cDenovo Ref SNPs for R =  336"
[1] "Number cDenovo Non-Ref SNPs for R =  1526"
[1] "Number cDenovo iSNPs for R =  0"
[1] "Number cDenovo Ref SNPs for V =  335"
[1] "Number cDenovo Non-Ref SNPs for V =  1531"
[1] "Number cDenovo iSNPs for V =  1"
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Subject 32

SNP_analysis_pipeline(subject_id = 32)

[1] "SUBJECT_ID is 32"
[1] "Rare iSNP cutoff =  3"
[1] "num rare iSNPs =  4383"
[1] "num common iSNPs =  4970"
[1] "Recombination block cutoff = 3"
[1] "Num bases in C recomb blocks=  1680"
[1] "Num bases in R recomb = blocks 1500"
[1] "Num bases in V recomb = blocks 82373"
[1] "Coverage cutoff =  10"
[1] "Numbers of R bases above cutoff is  1035511"
[1] "Numbers of C bases above cutoff is  939599"
[1] "Numbers of V bases above cutoff is  1036507"
[1] "Number of iSNP positions =  5168"
[1] "R only fixed SNPs (RonlyF) =  0"
[1] "R only rare fixed SNPs (RonlyFrare) =  0"
[1] "R only fixed SNPs in recombinant regions (RonlyFrecomb) =  0"
[1] "R only iSNPs (RonlyRI) =  13"
[1] "R only rare iSNPs (RonlyRIrare) =  1"
[1] "R only iSNPs in recombinant regions (RonlyRIrecomb) =  13"
[1] "C only fixed SNPs (ConlyF) =  0"
[1] "C only rare fixed SNPs (ConlyFrare) =  0"
[1] "C only fixed SNPs in recombinant regions (ConlyFrecomb) =  0"
[1] "C only iSNPs (ConlyRI) =  23"
[1] "C only rare iSNPs (ConlyRIrare) =  20"
[1] "C only iSNPs in recombinant regions (ConlyRIrecomb) =  1"
[1] "V only fixed SNPs (VonlyF) =  0"
[1] "V only rare fixed SNPs (VonlyFrare) =  0"
[1] "V only fixed SNPs in recombinant regions (VonlyFrecombb) =  0"
[1] "V only iSNPs (VonlyRI) =  576"
[1] "V only rare iSNPs (VonlyRIrare) =  266"
[1] "V only iSNPs in recombinant regions (VonlyRIrecomb) =  74"
[1] "RC only fixed SNPs (RConlyF) =  13"
[1] "RC only rare fixed SNPs (RConlyFrare) =  13"
[1] "RC only fixed SNPs in recombinant regions (RConlyFrecomb) =  0"
[1] "RC only iSNPs (RConlyRI) =  1"
[1] "RC only rare iSNPs (RConlyRIrare) =  0"
[1] "RC only iSNPs in recombinant regions (RConlyRIrecomb) =  0"
[1] "RV only fixed SNPs (RVonlyF) =  0"
[1] "RV only rare fixed SNPs (RVonlyFrare) =  0"
[1] "RV only fixed SNPs in recombinant regions (RVonlyFrecomb) =  0"
[1] "RV only iSNPs (RVonlyRI) =  1"
[1] "RV only rare iSNPs (RVonlyRIrare) =  0"
[1] "RV only iSNPs in recombinant regions (RVonlyRIrecomb) =  0"
[1] "VC only fixed SNPs (VConlyF) =  0"
[1] "VC only rare fixed SNPs (VConlyFrare) =  0"
[1] "VC only fixed SNPs in recombinant regions (VConlyFrecomb) =  0"
[1] "VC only iSNPs (VConlyRI) =  1"
[1] "VC only rare iSNPs (VConlyRIrare) =  0"
[1] "VC only iSNPs in recombinant regions (VConlyRIrecomb) =  0"
[1] "All fixed SNPs (AllF) =  726"
[1] "All rare fixed SNPs (AllFrare) =  508"
[1] "All fixed SNPs in recombinant regions (AllFrecomb) =  332"
[1] "All iSNPs (AllRI) =  11"
[1] "All rare  iSNPs (AllRIrare) =  0"
[1] "All iSNPs in recombinant regions (AllRIrecomb) =  1"
[1] "R is fixed, V only is intermediate, and rare (RonlyF_VIrare) =  0"
[1] "R is fixed, C only is intermediate, and rare (RonlyF_CIrare) =  0"
[1] "R is fixed, V and C are intermediate, and rare (RonlyF_CandVIrare) =  1"
[1] "C is fixed, V only is intermediate, and rare (ConlyF_VIrare) =  0"
[1] "C is fixed, R only is intermediate, and rare (ConlyF_RIrare) =  0"
[1] "C is fixed, R and V are intermediate, and rare (ConlyF_RandVIrare) =  0"
[1] "V is fixed, C only is intermediate, and rare (VonlyF_CIrare) =  0"
[1] "V is fixed, R only is intermediate, and rare (VonlyF_RIrare) =  0"
[1] "V is fixed, R and C are intermediate, and rare (VonlyF_CandRIrare) =  0"
[1] "R and C are fixed, V is intermediate, and rare (RCF_VIrare) =  416"
[1] "R and V are fixed, C is intermediate, and rare (RVF_CIrare) =  1"
[1] "V and C are fixed, R is intermediate, and rare (CVF_RIrare) =  0"

Warning: Removed 161 rows containing missing values (geom_point).
Warning: Removed 6 rows containing missing values (geom_point).
Warning: Removed 4 rows containing missing values (geom_point).
Warning: Removed 171 rows containing non-finite values (stat_boxplot).

[1] "Number cDenovo Ref SNPs for C =  318"
[1] "Number cDenovo Non-Ref SNPs for C =  1388"
[1] "Number cDenovo iSNPs for C =  3"
[1] "Number cDenovo Ref SNPs for R =  339"
[1] "Number cDenovo Non-Ref SNPs for R =  1525"
[1] "Number cDenovo iSNPs for R =  0"
[1] "Number cDenovo Ref SNPs for V =  192"
[1] "Number cDenovo Non-Ref SNPs for V =  102"
[1] "Number cDenovo iSNPs for V =  1572"
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Subject 68

SNP_analysis_pipeline(subject_id = 68)

[1] "SUBJECT_ID is 68"
[1] "Rare iSNP cutoff =  3"
[1] "num rare iSNPs =  4383"
[1] "num common iSNPs =  4970"
[1] "Recombination block cutoff = 3"
[1] "Num bases in C recomb blocks=  66"
[1] "Num bases in R recomb = blocks 206"
[1] "Num bases in V recomb = blocks 0"
[1] "Coverage cutoff =  10"
[1] "Numbers of R bases above cutoff is  1033503"
[1] "Numbers of C bases above cutoff is  1035903"
[1] "Numbers of V bases above cutoff is  1034542"
[1] "Number of iSNP positions =  5247"
[1] "R only fixed SNPs (RonlyF) =  0"
[1] "R only rare fixed SNPs (RonlyFrare) =  0"
[1] "R only fixed SNPs in recombinant regions (RonlyFrecomb) =  0"
[1] "R only iSNPs (RonlyRI) =  6"
[1] "R only rare iSNPs (RonlyRIrare) =  1"
[1] "R only iSNPs in recombinant regions (RonlyRIrecomb) =  0"
[1] "C only fixed SNPs (ConlyF) =  0"
[1] "C only rare fixed SNPs (ConlyFrare) =  0"
[1] "C only fixed SNPs in recombinant regions (ConlyFrecomb) =  0"
[1] "C only iSNPs (ConlyRI) =  1"
[1] "C only rare iSNPs (ConlyRIrare) =  1"
[1] "C only iSNPs in recombinant regions (ConlyRIrecomb) =  0"
[1] "V only fixed SNPs (VonlyF) =  0"
[1] "V only rare fixed SNPs (VonlyFrare) =  0"
[1] "V only fixed SNPs in recombinant regions (VonlyFrecombb) =  0"
[1] "V only iSNPs (VonlyRI) =  4"
[1] "V only rare iSNPs (VonlyRIrare) =  2"
[1] "V only iSNPs in recombinant regions (VonlyRIrecomb) =  0"
[1] "RC only fixed SNPs (RConlyF) =  0"
[1] "RC only rare fixed SNPs (RConlyFrare) =  0"
[1] "RC only fixed SNPs in recombinant regions (RConlyFrecomb) =  0"
[1] "RC only iSNPs (RConlyRI) =  0"
[1] "RC only rare iSNPs (RConlyRIrare) =  0"
[1] "RC only iSNPs in recombinant regions (RConlyRIrecomb) =  0"
[1] "RV only fixed SNPs (RVonlyF) =  0"
[1] "RV only rare fixed SNPs (RVonlyFrare) =  0"
[1] "RV only fixed SNPs in recombinant regions (RVonlyFrecomb) =  0"
[1] "RV only iSNPs (RVonlyRI) =  2"
[1] "RV only rare iSNPs (RVonlyRIrare) =  0"
[1] "RV only iSNPs in recombinant regions (RVonlyRIrecomb) =  0"
[1] "VC only fixed SNPs (VConlyF) =  0"
[1] "VC only rare fixed SNPs (VConlyFrare) =  0"
[1] "VC only fixed SNPs in recombinant regions (VConlyFrecomb) =  0"
[1] "VC only iSNPs (VConlyRI) =  2"
[1] "VC only rare iSNPs (VConlyRIrare) =  1"
[1] "VC only iSNPs in recombinant regions (VConlyRIrecomb) =  0"
[1] "All fixed SNPs (AllF) =  5189"
[1] "All rare fixed SNPs (AllFrare) =  1006"
[1] "All fixed SNPs in recombinant regions (AllFrecomb) =  0"
[1] "All iSNPs (AllRI) =  11"
[1] "All rare  iSNPs (AllRIrare) =  0"
[1] "All iSNPs in recombinant regions (AllRIrecomb) =  0"
[1] "R is fixed, V only is intermediate, and rare (RonlyF_VIrare) =  0"
[1] "R is fixed, C only is intermediate, and rare (RonlyF_CIrare) =  0"
[1] "R is fixed, V and C are intermediate, and rare (RonlyF_CandVIrare) =  0"
[1] "C is fixed, V only is intermediate, and rare (ConlyF_VIrare) =  0"
[1] "C is fixed, R only is intermediate, and rare (ConlyF_RIrare) =  0"
[1] "C is fixed, R and V are intermediate, and rare (ConlyF_RandVIrare) =  0"
[1] "V is fixed, C only is intermediate, and rare (VonlyF_CIrare) =  0"
[1] "V is fixed, R only is intermediate, and rare (VonlyF_RIrare) =  0"
[1] "V is fixed, R and C are intermediate, and rare (VonlyF_CandRIrare) =  0"
[1] "R and C are fixed, V is intermediate, and rare (RCF_VIrare) =  6"
[1] "R and V are fixed, C is intermediate, and rare (RVF_CIrare) =  0"
[1] "V and C are fixed, R is intermediate, and rare (CVF_RIrare) =  1"

Warning: Removed 4 rows containing missing values (geom_point).
Warning: Removed 6 rows containing missing values (geom_point).
Warning: Removed 2 rows containing missing values (geom_point).
Warning: Removed 12 rows containing non-finite values (stat_boxplot).

[1] "Number cDenovo Ref SNPs for C =  340"
[1] "Number cDenovo Non-Ref SNPs for C =  1527"
[1] "Number cDenovo iSNPs for C =  0"
[1] "Number cDenovo Ref SNPs for R =  337"
[1] "Number cDenovo Non-Ref SNPs for R =  1528"
[1] "Number cDenovo iSNPs for R =  0"
[1] "Number cDenovo Ref SNPs for V =  341"
[1] "Number cDenovo Non-Ref SNPs for V =  1526"
[1] "Number cDenovo iSNPs for V =  2"
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Subject 72

SNP_analysis_pipeline(subject_id = 72)

[1] "SUBJECT_ID is 72"
[1] "Rare iSNP cutoff =  3"
[1] "num rare iSNPs =  4383"
[1] "num common iSNPs =  4970"
[1] "Recombination block cutoff = 3"
[1] "Num bases in C recomb blocks=  73594"
[1] "Num bases in R recomb = blocks 72610"
[1] "Num bases in V recomb = blocks 44984"
[1] "Coverage cutoff =  10"
[1] "Numbers of R bases above cutoff is  344563"
[1] "Numbers of C bases above cutoff is  1011352"
[1] "Numbers of V bases above cutoff is  1029389"
[1] "Number of iSNP positions =  617"
[1] "R only fixed SNPs (RonlyF) =  0"
[1] "R only rare fixed SNPs (RonlyFrare) =  0"
[1] "R only fixed SNPs in recombinant regions (RonlyFrecomb) =  0"
[1] "R only iSNPs (RonlyRI) =  49"
[1] "R only rare iSNPs (RonlyRIrare) =  44"
[1] "R only iSNPs in recombinant regions (RonlyRIrecomb) =  0"
[1] "C only fixed SNPs (ConlyF) =  0"
[1] "C only rare fixed SNPs (ConlyFrare) =  0"
[1] "C only fixed SNPs in recombinant regions (ConlyFrecomb) =  0"
[1] "C only iSNPs (ConlyRI) =  0"
[1] "C only rare iSNPs (ConlyRIrare) =  0"
[1] "C only iSNPs in recombinant regions (ConlyRIrecomb) =  0"
[1] "V only fixed SNPs (VonlyF) =  0"
[1] "V only rare fixed SNPs (VonlyFrare) =  0"
[1] "V only fixed SNPs in recombinant regions (VonlyFrecombb) =  0"
[1] "V only iSNPs (VonlyRI) =  35"
[1] "V only rare iSNPs (VonlyRIrare) =  22"
[1] "V only iSNPs in recombinant regions (VonlyRIrecomb) =  1"
[1] "RC only fixed SNPs (RConlyF) =  0"
[1] "RC only rare fixed SNPs (RConlyFrare) =  0"
[1] "RC only fixed SNPs in recombinant regions (RConlyFrecomb) =  0"
[1] "RC only iSNPs (RConlyRI) =  0"
[1] "RC only rare iSNPs (RConlyRIrare) =  0"
[1] "RC only iSNPs in recombinant regions (RConlyRIrecomb) =  0"
[1] "RV only fixed SNPs (RVonlyF) =  0"
[1] "RV only rare fixed SNPs (RVonlyFrare) =  0"
[1] "RV only fixed SNPs in recombinant regions (RVonlyFrecomb) =  0"
[1] "RV only iSNPs (RVonlyRI) =  9"
[1] "RV only rare iSNPs (RVonlyRIrare) =  1"
[1] "RV only iSNPs in recombinant regions (RVonlyRIrecomb) =  1"
[1] "VC only fixed SNPs (VConlyF) =  0"
[1] "VC only rare fixed SNPs (VConlyFrare) =  0"
[1] "VC only fixed SNPs in recombinant regions (VConlyFrecomb) =  0"
[1] "VC only iSNPs (VConlyRI) =  1"
[1] "VC only rare iSNPs (VConlyRIrare) =  1"
[1] "VC only iSNPs in recombinant regions (VConlyRIrecomb) =  1"
[1] "All fixed SNPs (AllF) =  512"
[1] "All rare fixed SNPs (AllFrare) =  295"
[1] "All fixed SNPs in recombinant regions (AllFrecomb) =  104"
[1] "All iSNPs (AllRI) =  1"
[1] "All rare  iSNPs (AllRIrare) =  0"
[1] "All iSNPs in recombinant regions (AllRIrecomb) =  0"
[1] "R is fixed, V only is intermediate, and rare (RonlyF_VIrare) =  0"
[1] "R is fixed, C only is intermediate, and rare (RonlyF_CIrare) =  0"
[1] "R is fixed, V and C are intermediate, and rare (RonlyF_CandVIrare) =  0"
[1] "C is fixed, V only is intermediate, and rare (ConlyF_VIrare) =  0"
[1] "C is fixed, R only is intermediate, and rare (ConlyF_RIrare) =  0"
[1] "C is fixed, R and V are intermediate, and rare (ConlyF_RandVIrare) =  0"
[1] "V is fixed, C only is intermediate, and rare (VonlyF_CIrare) =  0"
[1] "V is fixed, R only is intermediate, and rare (VonlyF_RIrare) =  0"
[1] "V is fixed, R and C are intermediate, and rare (VonlyF_CandRIrare) =  0"
[1] "R and C are fixed, V is intermediate, and rare (RCF_VIrare) =  0"
[1] "R and V are fixed, C is intermediate, and rare (RVF_CIrare) =  0"
[1] "V and C are fixed, R is intermediate, and rare (CVF_RIrare) =  0"

Warning: Removed 59 rows containing missing values (geom_point).
Warning: Removed 1254 rows containing missing values (geom_point).
Warning: Removed 26 rows containing missing values (geom_point).
Warning: Removed 1339 rows containing non-finite values (stat_boxplot).

[1] "Number cDenovo Ref SNPs for C =  1570"
[1] "Number cDenovo Non-Ref SNPs for C =  243"
[1] "Number cDenovo iSNPs for C =  0"
[1] "Number cDenovo Ref SNPs for R =  542"
[1] "Number cDenovo Non-Ref SNPs for R =  76"
[1] "Number cDenovo iSNPs for R =  0"
[1] "Number cDenovo Ref SNPs for V =  1600"
[1] "Number cDenovo Non-Ref SNPs for V =  246"
[1] "Number cDenovo iSNPs for V =  0"
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Subject 87

SNP_analysis_pipeline(subject_id = 87)

[1] "SUBJECT_ID is 87"
[1] "Rare iSNP cutoff =  3"
[1] "num rare iSNPs =  4383"
[1] "num common iSNPs =  4970"
[1] "Recombination block cutoff = 3"
[1] "Num bases in C recomb blocks=  0"
[1] "Num bases in R recomb = blocks 0"
[1] "Num bases in V recomb = blocks 0"
[1] "Coverage cutoff =  10"
[1] "Numbers of R bases above cutoff is  1016254"
[1] "Numbers of C bases above cutoff is  1035662"
[1] "Numbers of V bases above cutoff is  1025249"
[1] "Number of iSNP positions =  1200"
[1] "R only fixed SNPs (RonlyF) =  0"
[1] "R only rare fixed SNPs (RonlyFrare) =  0"
[1] "R only fixed SNPs in recombinant regions (RonlyFrecomb) =  0"
[1] "R only iSNPs (RonlyRI) =  77"
[1] "R only rare iSNPs (RonlyRIrare) =  55"
[1] "R only iSNPs in recombinant regions (RonlyRIrecomb) =  0"
[1] "C only fixed SNPs (ConlyF) =  0"
[1] "C only rare fixed SNPs (ConlyFrare) =  0"
[1] "C only fixed SNPs in recombinant regions (ConlyFrecomb) =  0"
[1] "C only iSNPs (ConlyRI) =  3"
[1] "C only rare iSNPs (ConlyRIrare) =  3"
[1] "C only iSNPs in recombinant regions (ConlyRIrecomb) =  0"
[1] "V only fixed SNPs (VonlyF) =  0"
[1] "V only rare fixed SNPs (VonlyFrare) =  0"
[1] "V only fixed SNPs in recombinant regions (VonlyFrecombb) =  0"
[1] "V only iSNPs (VonlyRI) =  61"
[1] "V only rare iSNPs (VonlyRIrare) =  40"
[1] "V only iSNPs in recombinant regions (VonlyRIrecomb) =  0"
[1] "RC only fixed SNPs (RConlyF) =  0"
[1] "RC only rare fixed SNPs (RConlyFrare) =  0"
[1] "RC only fixed SNPs in recombinant regions (RConlyFrecomb) =  0"
[1] "RC only iSNPs (RConlyRI) =  2"
[1] "RC only rare iSNPs (RConlyRIrare) =  0"
[1] "RC only iSNPs in recombinant regions (RConlyRIrecomb) =  0"
[1] "RV only fixed SNPs (RVonlyF) =  0"
[1] "RV only rare fixed SNPs (RVonlyFrare) =  0"
[1] "RV only fixed SNPs in recombinant regions (RVonlyFrecomb) =  0"
[1] "RV only iSNPs (RVonlyRI) =  1"
[1] "RV only rare iSNPs (RVonlyRIrare) =  0"
[1] "RV only iSNPs in recombinant regions (RVonlyRIrecomb) =  0"
[1] "VC only fixed SNPs (VConlyF) =  0"
[1] "VC only rare fixed SNPs (VConlyFrare) =  0"
[1] "VC only fixed SNPs in recombinant regions (VConlyFrecomb) =  0"
[1] "VC only iSNPs (VConlyRI) =  3"
[1] "VC only rare iSNPs (VConlyRIrare) =  0"
[1] "VC only iSNPs in recombinant regions (VConlyRIrecomb) =  0"
[1] "All fixed SNPs (AllF) =  992"
[1] "All rare fixed SNPs (AllFrare) =  690"
[1] "All fixed SNPs in recombinant regions (AllFrecomb) =  0"
[1] "All iSNPs (AllRI) =  1"
[1] "All rare  iSNPs (AllRIrare) =  0"
[1] "All iSNPs in recombinant regions (AllRIrecomb) =  0"
[1] "R is fixed, V only is intermediate, and rare (RonlyF_VIrare) =  0"
[1] "R is fixed, C only is intermediate, and rare (RonlyF_CIrare) =  0"
[1] "R is fixed, V and C are intermediate, and rare (RonlyF_CandVIrare) =  0"
[1] "C is fixed, V only is intermediate, and rare (ConlyF_VIrare) =  1"
[1] "C is fixed, R only is intermediate, and rare (ConlyF_RIrare) =  0"
[1] "C is fixed, R and V are intermediate, and rare (ConlyF_RandVIrare) =  0"
[1] "V is fixed, C only is intermediate, and rare (VonlyF_CIrare) =  0"
[1] "V is fixed, R only is intermediate, and rare (VonlyF_RIrare) =  0"
[1] "V is fixed, R and C are intermediate, and rare (VonlyF_CandRIrare) =  0"
[1] "R and C are fixed, V is intermediate, and rare (RCF_VIrare) =  4"
[1] "R and V are fixed, C is intermediate, and rare (RVF_CIrare) =  0"
[1] "V and C are fixed, R is intermediate, and rare (CVF_RIrare) =  5"

Warning: Removed 15 rows containing missing values (geom_point).
Warning: Removed 49 rows containing missing values (geom_point).
Warning: Removed 24 rows containing missing values (geom_point).
Warning: Removed 88 rows containing non-finite values (stat_boxplot).

[1] "Number cDenovo Ref SNPs for C =  1589"
[1] "Number cDenovo Non-Ref SNPs for C =  268"
[1] "Number cDenovo iSNPs for C =  0"
[1] "Number cDenovo Ref SNPs for R =  1550"
[1] "Number cDenovo Non-Ref SNPs for R =  257"
[1] "Number cDenovo iSNPs for R =  16"
[1] "Number cDenovo Ref SNPs for V =  1574"
[1] "Number cDenovo Non-Ref SNPs for V =  263"
[1] "Number cDenovo iSNPs for V =  11"
[[1]]

[[2]]

[[3]]

[[4]]

[[5]]

[[6]]

[[7]]

[[8]]

[[9]]

Subject 98

SNP_analysis_pipeline(subject_id = 98)

[1] "SUBJECT_ID is 98"
[1] "Rare iSNP cutoff =  3"
[1] "num rare iSNPs =  4383"
[1] "num common iSNPs =  4970"
[1] "Recombination block cutoff = 3"
[1] "Num bases in C recomb blocks=  0"
[1] "Num bases in R recomb = blocks 0"
[1] "Num bases in V recomb = blocks 0"
[1] "Coverage cutoff =  10"
[1] "Numbers of R bases above cutoff is  1038078"
[1] "Numbers of C bases above cutoff is  1004338"
[1] "Numbers of V bases above cutoff is  1035500"
[1] "Number of iSNP positions =  1301"
[1] "R only fixed SNPs (RonlyF) =  0"
[1] "R only rare fixed SNPs (RonlyFrare) =  0"
[1] "R only fixed SNPs in recombinant regions (RonlyFrecomb) =  0"
[1] "R only iSNPs (RonlyRI) =  27"
[1] "R only rare iSNPs (RonlyRIrare) =  15"
[1] "R only iSNPs in recombinant regions (RonlyRIrecomb) =  0"
[1] "C only fixed SNPs (ConlyF) =  0"
[1] "C only rare fixed SNPs (ConlyFrare) =  0"
[1] "C only fixed SNPs in recombinant regions (ConlyFrecomb) =  0"
[1] "C only iSNPs (ConlyRI) =  2"
[1] "C only rare iSNPs (ConlyRIrare) =  2"
[1] "C only iSNPs in recombinant regions (ConlyRIrecomb) =  0"
[1] "V only fixed SNPs (VonlyF) =  0"
[1] "V only rare fixed SNPs (VonlyFrare) =  0"
[1] "V only fixed SNPs in recombinant regions (VonlyFrecombb) =  0"
[1] "V only iSNPs (VonlyRI) =  47"
[1] "V only rare iSNPs (VonlyRIrare) =  39"
[1] "V only iSNPs in recombinant regions (VonlyRIrecomb) =  0"
[1] "RC only fixed SNPs (RConlyF) =  0"
[1] "RC only rare fixed SNPs (RConlyFrare) =  0"
[1] "RC only fixed SNPs in recombinant regions (RConlyFrecomb) =  0"
[1] "RC only iSNPs (RConlyRI) =  0"
[1] "RC only rare iSNPs (RConlyRIrare) =  0"
[1] "RC only iSNPs in recombinant regions (RConlyRIrecomb) =  0"
[1] "RV only fixed SNPs (RVonlyF) =  0"
[1] "RV only rare fixed SNPs (RVonlyFrare) =  0"
[1] "RV only fixed SNPs in recombinant regions (RVonlyFrecomb) =  0"
[1] "RV only iSNPs (RVonlyRI) =  31"
[1] "RV only rare iSNPs (RVonlyRIrare) =  3"
[1] "RV only iSNPs in recombinant regions (RVonlyRIrecomb) =  0"
[1] "VC only fixed SNPs (VConlyF) =  0"
[1] "VC only rare fixed SNPs (VConlyFrare) =  0"
[1] "VC only fixed SNPs in recombinant regions (VConlyFrecomb) =  0"
[1] "VC only iSNPs (VConlyRI) =  0"
[1] "VC only rare iSNPs (VConlyRIrare) =  0"
[1] "VC only iSNPs in recombinant regions (VConlyRIrecomb) =  0"
[1] "All fixed SNPs (AllF) =  1159"
[1] "All rare fixed SNPs (AllFrare) =  792"
[1] "All fixed SNPs in recombinant regions (AllFrecomb) =  0"
[1] "All iSNPs (AllRI) =  3"
[1] "All rare  iSNPs (AllRIrare) =  0"
[1] "All iSNPs in recombinant regions (AllRIrecomb) =  0"
[1] "R is fixed, V only is intermediate, and rare (RonlyF_VIrare) =  0"
[1] "R is fixed, C only is intermediate, and rare (RonlyF_CIrare) =  0"
[1] "R is fixed, V and C are intermediate, and rare (RonlyF_CandVIrare) =  0"
[1] "C is fixed, V only is intermediate, and rare (ConlyF_VIrare) =  0"
[1] "C is fixed, R only is intermediate, and rare (ConlyF_RIrare) =  0"
[1] "C is fixed, R and V are intermediate, and rare (ConlyF_RandVIrare) =  0"
[1] "V is fixed, C only is intermediate, and rare (VonlyF_CIrare) =  0"
[1] "V is fixed, R only is intermediate, and rare (VonlyF_RIrare) =  0"
[1] "V is fixed, R and C are intermediate, and rare (VonlyF_CandRIrare) =  0"
[1] "R and C are fixed, V is intermediate, and rare (RCF_VIrare) =  0"
[1] "R and V are fixed, C is intermediate, and rare (RVF_CIrare) =  13"
[1] "V and C are fixed, R is intermediate, and rare (CVF_RIrare) =  0"

Warning: Removed 79 rows containing missing values (geom_point).
Warning: Removed 3 rows containing missing values (geom_point).
Warning: Removed 5 rows containing missing values (geom_point).
Warning: Removed 87 rows containing non-finite values (stat_boxplot).

[1] "Number cDenovo Ref SNPs for C =  1552"
[1] "Number cDenovo Non-Ref SNPs for C =  241"
[1] "Number cDenovo iSNPs for C =  0"
[1] "Number cDenovo Ref SNPs for R =  1610"
[1] "Number cDenovo Non-Ref SNPs for R =  259"
[1] "Number cDenovo iSNPs for R =  0"
[1] "Number cDenovo Ref SNPs for V =  1611"
[1] "Number cDenovo Non-Ref SNPs for V =  256"
[1] "Number cDenovo iSNPs for V =  0"
[[1]]

[[2]]

[[3]]

[[4]]

[[5]]

[[6]]

[[7]]

[[8]]

[[9]]

Subject 107

SNP_analysis_pipeline(subject_id = 107)

[1] "SUBJECT_ID is 107"
[1] "Rare iSNP cutoff =  3"
[1] "num rare iSNPs =  4383"
[1] "num common iSNPs =  4970"
[1] "Recombination block cutoff = 3"
[1] "Num bases in C recomb blocks=  951"
[1] "Num bases in R recomb = blocks 951"
[1] "Num bases in V recomb = blocks 0"
[1] "Coverage cutoff =  10"
[1] "Numbers of R bases above cutoff is  1036634"
[1] "Numbers of C bases above cutoff is  792534"
[1] "Numbers of V bases above cutoff is  1029789"
[1] "Number of iSNP positions =  3726"
[1] "R only fixed SNPs (RonlyF) =  2"
[1] "R only rare fixed SNPs (RonlyFrare) =  2"
[1] "R only fixed SNPs in recombinant regions (RonlyFrecomb) =  0"
[1] "R only iSNPs (RonlyRI) =  34"
[1] "R only rare iSNPs (RonlyRIrare) =  13"
[1] "R only iSNPs in recombinant regions (RonlyRIrecomb) =  0"
[1] "C only fixed SNPs (ConlyF) =  0"
[1] "C only rare fixed SNPs (ConlyFrare) =  0"
[1] "C only fixed SNPs in recombinant regions (ConlyFrecomb) =  0"
[1] "C only iSNPs (ConlyRI) =  34"
[1] "C only rare iSNPs (ConlyRIrare) =  34"
[1] "C only iSNPs in recombinant regions (ConlyRIrecomb) =  0"
[1] "V only fixed SNPs (VonlyF) =  0"
[1] "V only rare fixed SNPs (VonlyFrare) =  0"
[1] "V only fixed SNPs in recombinant regions (VonlyFrecombb) =  0"
[1] "V only iSNPs (VonlyRI) =  65"
[1] "V only rare iSNPs (VonlyRIrare) =  51"
[1] "V only iSNPs in recombinant regions (VonlyRIrecomb) =  0"
[1] "RC only fixed SNPs (RConlyF) =  0"
[1] "RC only rare fixed SNPs (RConlyFrare) =  0"
[1] "RC only fixed SNPs in recombinant regions (RConlyFrecomb) =  0"
[1] "RC only iSNPs (RConlyRI) =  0"
[1] "RC only rare iSNPs (RConlyRIrare) =  0"
[1] "RC only iSNPs in recombinant regions (RConlyRIrecomb) =  0"
[1] "RV only fixed SNPs (RVonlyF) =  0"
[1] "RV only rare fixed SNPs (RVonlyFrare) =  0"
[1] "RV only fixed SNPs in recombinant regions (RVonlyFrecomb) =  0"
[1] "RV only iSNPs (RVonlyRI) =  25"
[1] "RV only rare iSNPs (RVonlyRIrare) =  4"
[1] "RV only iSNPs in recombinant regions (RVonlyRIrecomb) =  0"
[1] "VC only fixed SNPs (VConlyF) =  0"
[1] "VC only rare fixed SNPs (VConlyFrare) =  0"
[1] "VC only fixed SNPs in recombinant regions (VConlyFrecomb) =  0"
[1] "VC only iSNPs (VConlyRI) =  0"
[1] "VC only rare iSNPs (VConlyRIrare) =  0"
[1] "VC only iSNPs in recombinant regions (VConlyRIrecomb) =  0"
[1] "All fixed SNPs (AllF) =  3546"
[1] "All rare fixed SNPs (AllFrare) =  674"
[1] "All fixed SNPs in recombinant regions (AllFrecomb) =  32"
[1] "All iSNPs (AllRI) =  0"
[1] "All rare  iSNPs (AllRIrare) =  0"
[1] "All iSNPs in recombinant regions (AllRIrecomb) =  0"
[1] "R is fixed, V only is intermediate, and rare (RonlyF_VIrare) =  0"
[1] "R is fixed, C only is intermediate, and rare (RonlyF_CIrare) =  0"
[1] "R is fixed, V and C are intermediate, and rare (RonlyF_CandVIrare) =  0"
[1] "C is fixed, V only is intermediate, and rare (ConlyF_VIrare) =  0"
[1] "C is fixed, R only is intermediate, and rare (ConlyF_RIrare) =  0"
[1] "C is fixed, R and V are intermediate, and rare (ConlyF_RandVIrare) =  0"
[1] "V is fixed, C only is intermediate, and rare (VonlyF_CIrare) =  0"
[1] "V is fixed, R only is intermediate, and rare (VonlyF_RIrare) =  0"
[1] "V is fixed, R and C are intermediate, and rare (VonlyF_CandRIrare) =  0"
[1] "R and C are fixed, V is intermediate, and rare (RCF_VIrare) =  0"
[1] "R and V are fixed, C is intermediate, and rare (RVF_CIrare) =  0"
[1] "V and C are fixed, R is intermediate, and rare (CVF_RIrare) =  0"

Warning: Removed 276 rows containing missing values (geom_point).
Warning: Removed 14 rows containing missing values (geom_point).
Warning: Removed 15 rows containing missing values (geom_point).
Warning: Removed 305 rows containing non-finite values (stat_boxplot).

[1] "Number cDenovo Ref SNPs for C =  291"
[1] "Number cDenovo Non-Ref SNPs for C =  1304"
[1] "Number cDenovo iSNPs for C =  0"
[1] "Number cDenovo Ref SNPs for R =  337"
[1] "Number cDenovo Non-Ref SNPs for R =  1520"
[1] "Number cDenovo iSNPs for R =  0"
[1] "Number cDenovo Ref SNPs for V =  338"
[1] "Number cDenovo Non-Ref SNPs for V =  1518"
[1] "Number cDenovo iSNPs for V =  0"
[[1]]

[[2]]

[[3]]

[[4]]

[[5]]

[[6]]

[[7]]

[[8]]

[[9]]

Subject 192

SNP_analysis_pipeline(subject_id = 192)

[1] "SUBJECT_ID is 192"
[1] "Rare iSNP cutoff =  3"
[1] "num rare iSNPs =  4383"
[1] "num common iSNPs =  4970"
[1] "Recombination block cutoff = 3"
[1] "Num bases in C recomb blocks=  47748"
[1] "Num bases in R recomb = blocks 47523"
[1] "Num bases in V recomb = blocks 47523"
[1] "Coverage cutoff =  10"
[1] "Numbers of R bases above cutoff is  1036095"
[1] "Numbers of C bases above cutoff is  1028769"
[1] "Numbers of V bases above cutoff is  1037030"
[1] "Number of iSNP positions =  5297"
[1] "R only fixed SNPs (RonlyF) =  1"
[1] "R only rare fixed SNPs (RonlyFrare) =  1"
[1] "R only fixed SNPs in recombinant regions (RonlyFrecomb) =  0"
[1] "R only iSNPs (RonlyRI) =  20"
[1] "R only rare iSNPs (RonlyRIrare) =  13"
[1] "R only iSNPs in recombinant regions (RonlyRIrecomb) =  0"
[1] "C only fixed SNPs (ConlyF) =  0"
[1] "C only rare fixed SNPs (ConlyFrare) =  0"
[1] "C only fixed SNPs in recombinant regions (ConlyFrecomb) =  0"
[1] "C only iSNPs (ConlyRI) =  2"
[1] "C only rare iSNPs (ConlyRIrare) =  2"
[1] "C only iSNPs in recombinant regions (ConlyRIrecomb) =  1"
[1] "V only fixed SNPs (VonlyF) =  0"
[1] "V only rare fixed SNPs (VonlyFrare) =  0"
[1] "V only fixed SNPs in recombinant regions (VonlyFrecombb) =  0"
[1] "V only iSNPs (VonlyRI) =  64"
[1] "V only rare iSNPs (VonlyRIrare) =  51"
[1] "V only iSNPs in recombinant regions (VonlyRIrecomb) =  3"
[1] "RC only fixed SNPs (RConlyF) =  0"
[1] "RC only rare fixed SNPs (RConlyFrare) =  0"
[1] "RC only fixed SNPs in recombinant regions (RConlyFrecomb) =  0"
[1] "RC only iSNPs (RConlyRI) =  0"
[1] "RC only rare iSNPs (RConlyRIrare) =  0"
[1] "RC only iSNPs in recombinant regions (RConlyRIrecomb) =  0"
[1] "RV only fixed SNPs (RVonlyF) =  2"
[1] "RV only rare fixed SNPs (RVonlyFrare) =  0"
[1] "RV only fixed SNPs in recombinant regions (RVonlyFrecomb) =  0"
[1] "RV only iSNPs (RVonlyRI) =  46"
[1] "RV only rare iSNPs (RVonlyRIrare) =  7"
[1] "RV only iSNPs in recombinant regions (RVonlyRIrecomb) =  1"
[1] "VC only fixed SNPs (VConlyF) =  0"
[1] "VC only rare fixed SNPs (VConlyFrare) =  0"
[1] "VC only fixed SNPs in recombinant regions (VConlyFrecomb) =  0"
[1] "VC only iSNPs (VConlyRI) =  1"
[1] "VC only rare iSNPs (VConlyRIrare) =  1"
[1] "VC only iSNPs in recombinant regions (VConlyRIrecomb) =  0"
[1] "All fixed SNPs (AllF) =  5115"
[1] "All rare fixed SNPs (AllFrare) =  1215"
[1] "All fixed SNPs in recombinant regions (AllFrecomb) =  81"
[1] "All iSNPs (AllRI) =  7"
[1] "All rare  iSNPs (AllRIrare) =  0"
[1] "All iSNPs in recombinant regions (AllRIrecomb) =  0"
[1] "R is fixed, V only is intermediate, and rare (RonlyF_VIrare) =  0"
[1] "R is fixed, C only is intermediate, and rare (RonlyF_CIrare) =  0"
[1] "R is fixed, V and C are intermediate, and rare (RonlyF_CandVIrare) =  0"
[1] "C is fixed, V only is intermediate, and rare (ConlyF_VIrare) =  0"
[1] "C is fixed, R only is intermediate, and rare (ConlyF_RIrare) =  0"
[1] "C is fixed, R and V are intermediate, and rare (ConlyF_RandVIrare) =  0"
[1] "V is fixed, C only is intermediate, and rare (VonlyF_CIrare) =  2"
[1] "V is fixed, R only is intermediate, and rare (VonlyF_RIrare) =  0"
[1] "V is fixed, R and C are intermediate, and rare (VonlyF_CandRIrare) =  0"
[1] "R and C are fixed, V is intermediate, and rare (RCF_VIrare) =  0"
[1] "R and V are fixed, C is intermediate, and rare (RVF_CIrare) =  4"
[1] "V and C are fixed, R is intermediate, and rare (CVF_RIrare) =  1"

Warning: Removed 18 rows containing missing values (geom_point).
Warning: Removed 10 rows containing missing values (geom_point).
Warning: Removed 2 rows containing missing values (geom_point).
Warning: Removed 30 rows containing non-finite values (stat_boxplot).

[1] "Number cDenovo Ref SNPs for C =  317"
[1] "Number cDenovo Non-Ref SNPs for C =  1534"
[1] "Number cDenovo iSNPs for C =  1"
[1] "Number cDenovo Ref SNPs for R =  321"
[1] "Number cDenovo Non-Ref SNPs for R =  1539"
[1] "Number cDenovo iSNPs for R =  0"
[1] "Number cDenovo Ref SNPs for V =  323"
[1] "Number cDenovo Non-Ref SNPs for V =  1545"
[1] "Number cDenovo iSNPs for V =  0"
[[1]]

[[2]]

[[3]]

[[4]]

[[5]]

[[6]]

[[7]]

[[8]]

[[9]]

Subject 227

SNP_analysis_pipeline(subject_id = 227)

[1] "SUBJECT_ID is 227"
[1] "Rare iSNP cutoff =  3"
[1] "num rare iSNPs =  4383"
[1] "num common iSNPs =  4970"
[1] "Recombination block cutoff = 3"
[1] "Num bases in C recomb blocks=  16439"
[1] "Num bases in R recomb = blocks 14887"
[1] "Num bases in V recomb = blocks 14887"
[1] "Coverage cutoff =  10"
[1] "Numbers of R bases above cutoff is  822591"
[1] "Numbers of C bases above cutoff is  1034715"
[1] "Numbers of V bases above cutoff is  1038235"
[1] "Number of iSNP positions =  999"
[1] "R only fixed SNPs (RonlyF) =  0"
[1] "R only rare fixed SNPs (RonlyFrare) =  0"
[1] "R only fixed SNPs in recombinant regions (RonlyFrecomb) =  0"
[1] "R only iSNPs (RonlyRI) =  178"
[1] "R only rare iSNPs (RonlyRIrare) =  149"
[1] "R only iSNPs in recombinant regions (RonlyRIrecomb) =  6"
[1] "C only fixed SNPs (ConlyF) =  0"
[1] "C only rare fixed SNPs (ConlyFrare) =  0"
[1] "C only fixed SNPs in recombinant regions (ConlyFrecomb) =  0"
[1] "C only iSNPs (ConlyRI) =  0"
[1] "C only rare iSNPs (ConlyRIrare) =  0"
[1] "C only iSNPs in recombinant regions (ConlyRIrecomb) =  0"
[1] "V only fixed SNPs (VonlyF) =  0"
[1] "V only rare fixed SNPs (VonlyFrare) =  0"
[1] "V only fixed SNPs in recombinant regions (VonlyFrecombb) =  0"
[1] "V only iSNPs (VonlyRI) =  0"
[1] "V only rare iSNPs (VonlyRIrare) =  0"
[1] "V only iSNPs in recombinant regions (VonlyRIrecomb) =  0"
[1] "RC only fixed SNPs (RConlyF) =  0"
[1] "RC only rare fixed SNPs (RConlyFrare) =  0"
[1] "RC only fixed SNPs in recombinant regions (RConlyFrecomb) =  0"
[1] "RC only iSNPs (RConlyRI) =  0"
[1] "RC only rare iSNPs (RConlyRIrare) =  0"
[1] "RC only iSNPs in recombinant regions (RConlyRIrecomb) =  0"
[1] "RV only fixed SNPs (RVonlyF) =  0"
[1] "RV only rare fixed SNPs (RVonlyFrare) =  0"
[1] "RV only fixed SNPs in recombinant regions (RVonlyFrecomb) =  0"
[1] "RV only iSNPs (RVonlyRI) =  0"
[1] "RV only rare iSNPs (RVonlyRIrare) =  0"
[1] "RV only iSNPs in recombinant regions (RVonlyRIrecomb) =  0"
[1] "VC only fixed SNPs (VConlyF) =  0"
[1] "VC only rare fixed SNPs (VConlyFrare) =  0"
[1] "VC only fixed SNPs in recombinant regions (VConlyFrecomb) =  0"
[1] "VC only iSNPs (VConlyRI) =  3"
[1] "VC only rare iSNPs (VConlyRIrare) =  1"
[1] "VC only iSNPs in recombinant regions (VConlyRIrecomb) =  0"
[1] "All fixed SNPs (AllF) =  798"
[1] "All rare fixed SNPs (AllFrare) =  540"
[1] "All fixed SNPs in recombinant regions (AllFrecomb) =  27"
[1] "All iSNPs (AllRI) =  4"
[1] "All rare  iSNPs (AllRIrare) =  0"
[1] "All iSNPs in recombinant regions (AllRIrecomb) =  0"
[1] "R is fixed, V only is intermediate, and rare (RonlyF_VIrare) =  0"
[1] "R is fixed, C only is intermediate, and rare (RonlyF_CIrare) =  0"
[1] "R is fixed, V and C are intermediate, and rare (RonlyF_CandVIrare) =  0"
[1] "C is fixed, V only is intermediate, and rare (ConlyF_VIrare) =  0"
[1] "C is fixed, R only is intermediate, and rare (ConlyF_RIrare) =  0"
[1] "C is fixed, R and V are intermediate, and rare (ConlyF_RandVIrare) =  0"
[1] "V is fixed, C only is intermediate, and rare (VonlyF_CIrare) =  0"
[1] "V is fixed, R only is intermediate, and rare (VonlyF_RIrare) =  0"
[1] "V is fixed, R and C are intermediate, and rare (VonlyF_CandRIrare) =  0"
[1] "R and C are fixed, V is intermediate, and rare (RCF_VIrare) =  0"
[1] "R and V are fixed, C is intermediate, and rare (RVF_CIrare) =  0"
[1] "V and C are fixed, R is intermediate, and rare (CVF_RIrare) =  0"

Warning: Removed 12 rows containing missing values (geom_point).
Warning: Removed 427 rows containing missing values (geom_point).
Warning: Removed 3 rows containing missing values (geom_point).
Warning: Removed 442 rows containing non-finite values (stat_boxplot).

[1] "Number cDenovo Ref SNPs for C =  1623"
[1] "Number cDenovo Non-Ref SNPs for C =  237"
[1] "Number cDenovo iSNPs for C =  0"
[1] "Number cDenovo Ref SNPs for R =  1257"
[1] "Number cDenovo Non-Ref SNPs for R =  179"
[1] "Number cDenovo iSNPs for R =  9"
[1] "Number cDenovo Ref SNPs for V =  1630"
[1] "Number cDenovo Non-Ref SNPs for V =  239"
[1] "Number cDenovo iSNPs for V =  0"
[[1]]

[[2]]

[[3]]

[[4]]

[[5]]

[[6]]

[[7]]

[[8]]

[[9]]

Subject 362

SNP_analysis_pipeline(subject_id = 362)

[1] "SUBJECT_ID is 362"
[1] "Rare iSNP cutoff =  3"
[1] "num rare iSNPs =  4383"
[1] "num common iSNPs =  4970"
[1] "Recombination block cutoff = 3"
[1] "Num bases in C recomb blocks=  168863"
[1] "Num bases in R recomb = blocks 168863"
[1] "Num bases in V recomb = blocks 168755"
[1] "Coverage cutoff =  10"
[1] "Numbers of R bases above cutoff is  1031572"
[1] "Numbers of C bases above cutoff is  1032552"
[1] "Numbers of V bases above cutoff is  1038383"
[1] "Number of iSNP positions =  2002"
[1] "R only fixed SNPs (RonlyF) =  0"
[1] "R only rare fixed SNPs (RonlyFrare) =  0"
[1] "R only fixed SNPs in recombinant regions (RonlyFrecomb) =  0"
[1] "R only iSNPs (RonlyRI) =  10"
[1] "R only rare iSNPs (RonlyRIrare) =  9"
[1] "R only iSNPs in recombinant regions (RonlyRIrecomb) =  1"
[1] "C only fixed SNPs (ConlyF) =  0"
[1] "C only rare fixed SNPs (ConlyFrare) =  0"
[1] "C only fixed SNPs in recombinant regions (ConlyFrecomb) =  0"
[1] "C only iSNPs (ConlyRI) =  4"
[1] "C only rare iSNPs (ConlyRIrare) =  4"
[1] "C only iSNPs in recombinant regions (ConlyRIrecomb) =  0"
[1] "V only fixed SNPs (VonlyF) =  0"
[1] "V only rare fixed SNPs (VonlyFrare) =  0"
[1] "V only fixed SNPs in recombinant regions (VonlyFrecombb) =  0"
[1] "V only iSNPs (VonlyRI) =  3"
[1] "V only rare iSNPs (VonlyRIrare) =  2"
[1] "V only iSNPs in recombinant regions (VonlyRIrecomb) =  0"
[1] "RC only fixed SNPs (RConlyF) =  0"
[1] "RC only rare fixed SNPs (RConlyFrare) =  0"
[1] "RC only fixed SNPs in recombinant regions (RConlyFrecomb) =  0"
[1] "RC only iSNPs (RConlyRI) =  0"
[1] "RC only rare iSNPs (RConlyRIrare) =  0"
[1] "RC only iSNPs in recombinant regions (RConlyRIrecomb) =  0"
[1] "RV only fixed SNPs (RVonlyF) =  0"
[1] "RV only rare fixed SNPs (RVonlyFrare) =  0"
[1] "RV only fixed SNPs in recombinant regions (RVonlyFrecomb) =  0"
[1] "RV only iSNPs (RVonlyRI) =  5"
[1] "RV only rare iSNPs (RVonlyRIrare) =  1"
[1] "RV only iSNPs in recombinant regions (RVonlyRIrecomb) =  1"
[1] "VC only fixed SNPs (VConlyF) =  0"
[1] "VC only rare fixed SNPs (VConlyFrare) =  0"
[1] "VC only fixed SNPs in recombinant regions (VConlyFrecomb) =  0"
[1] "VC only iSNPs (VConlyRI) =  1"
[1] "VC only rare iSNPs (VConlyRIrare) =  0"
[1] "VC only iSNPs in recombinant regions (VConlyRIrecomb) =  0"
[1] "All fixed SNPs (AllF) =  1944"
[1] "All rare fixed SNPs (AllFrare) =  879"
[1] "All fixed SNPs in recombinant regions (AllFrecomb) =  809"
[1] "All iSNPs (AllRI) =  13"
[1] "All rare  iSNPs (AllRIrare) =  1"
[1] "All iSNPs in recombinant regions (AllRIrecomb) =  2"
[1] "R is fixed, V only is intermediate, and rare (RonlyF_VIrare) =  0"
[1] "R is fixed, C only is intermediate, and rare (RonlyF_CIrare) =  0"
[1] "R is fixed, V and C are intermediate, and rare (RonlyF_CandVIrare) =  0"
[1] "C is fixed, V only is intermediate, and rare (ConlyF_VIrare) =  0"
[1] "C is fixed, R only is intermediate, and rare (ConlyF_RIrare) =  0"
[1] "C is fixed, R and V are intermediate, and rare (ConlyF_RandVIrare) =  0"
[1] "V is fixed, C only is intermediate, and rare (VonlyF_CIrare) =  0"
[1] "V is fixed, R only is intermediate, and rare (VonlyF_RIrare) =  0"
[1] "V is fixed, R and C are intermediate, and rare (VonlyF_CandRIrare) =  0"
[1] "R and C are fixed, V is intermediate, and rare (RCF_VIrare) =  2"
[1] "R and V are fixed, C is intermediate, and rare (RVF_CIrare) =  0"
[1] "V and C are fixed, R is intermediate, and rare (CVF_RIrare) =  2"

Warning: Removed 6 rows containing missing values (geom_point).
Warning: Removed 24 rows containing missing values (geom_point).
Warning: Removed 2 rows containing missing values (geom_point).
Warning: Removed 32 rows containing non-finite values (stat_boxplot).

[1] "Number cDenovo Ref SNPs for C =  1627"
[1] "Number cDenovo Non-Ref SNPs for C =  239"
[1] "Number cDenovo iSNPs for C =  0"
[1] "Number cDenovo Ref SNPs for R =  1611"
[1] "Number cDenovo Non-Ref SNPs for R =  236"
[1] "Number cDenovo iSNPs for R =  1"
[1] "Number cDenovo Ref SNPs for V =  1630"
[1] "Number cDenovo Non-Ref SNPs for V =  240"
[1] "Number cDenovo iSNPs for V =  0"
[[1]]

[[2]]

[[3]]

[[4]]

[[5]]

[[6]]

[[7]]

[[8]]

[[9]]

Subject 519

SNP_analysis_pipeline(subject_id = 519)

[1] "SUBJECT_ID is 519"
[1] "Rare iSNP cutoff =  3"
[1] "num rare iSNPs =  4383"
[1] "num common iSNPs =  4970"
[1] "Recombination block cutoff = 3"
[1] "Num bases in C recomb blocks=  395"
[1] "Num bases in R recomb = blocks 0"
[1] "Num bases in V recomb = blocks 226"
[1] "Coverage cutoff =  10"
[1] "Numbers of R bases above cutoff is  818552"
[1] "Numbers of C bases above cutoff is  1020321"
[1] "Numbers of V bases above cutoff is  1034717"
[1] "Number of iSNP positions =  3957"
[1] "R only fixed SNPs (RonlyF) =  0"
[1] "R only rare fixed SNPs (RonlyFrare) =  0"
[1] "R only fixed SNPs in recombinant regions (RonlyFrecomb) =  0"
[1] "R only iSNPs (RonlyRI) =  27"
[1] "R only rare iSNPs (RonlyRIrare) =  27"
[1] "R only iSNPs in recombinant regions (RonlyRIrecomb) =  0"
[1] "C only fixed SNPs (ConlyF) =  0"
[1] "C only rare fixed SNPs (ConlyFrare) =  0"
[1] "C only fixed SNPs in recombinant regions (ConlyFrecomb) =  0"
[1] "C only iSNPs (ConlyRI) =  1"
[1] "C only rare iSNPs (ConlyRIrare) =  0"
[1] "C only iSNPs in recombinant regions (ConlyRIrecomb) =  0"
[1] "V only fixed SNPs (VonlyF) =  0"
[1] "V only rare fixed SNPs (VonlyFrare) =  0"
[1] "V only fixed SNPs in recombinant regions (VonlyFrecombb) =  0"
[1] "V only iSNPs (VonlyRI) =  3"
[1] "V only rare iSNPs (VonlyRIrare) =  2"
[1] "V only iSNPs in recombinant regions (VonlyRIrecomb) =  0"
[1] "RC only fixed SNPs (RConlyF) =  0"
[1] "RC only rare fixed SNPs (RConlyFrare) =  0"
[1] "RC only fixed SNPs in recombinant regions (RConlyFrecomb) =  0"
[1] "RC only iSNPs (RConlyRI) =  0"
[1] "RC only rare iSNPs (RConlyRIrare) =  0"
[1] "RC only iSNPs in recombinant regions (RConlyRIrecomb) =  0"
[1] "RV only fixed SNPs (RVonlyF) =  0"
[1] "RV only rare fixed SNPs (RVonlyFrare) =  0"
[1] "RV only fixed SNPs in recombinant regions (RVonlyFrecomb) =  0"
[1] "RV only iSNPs (RVonlyRI) =  0"
[1] "RV only rare iSNPs (RVonlyRIrare) =  0"
[1] "RV only iSNPs in recombinant regions (RVonlyRIrecomb) =  0"
[1] "VC only fixed SNPs (VConlyF) =  0"
[1] "VC only rare fixed SNPs (VConlyFrare) =  0"
[1] "VC only fixed SNPs in recombinant regions (VConlyFrecomb) =  0"
[1] "VC only iSNPs (VConlyRI) =  0"
[1] "VC only rare iSNPs (VConlyRIrare) =  0"
[1] "VC only iSNPs in recombinant regions (VConlyRIrecomb) =  0"
[1] "All fixed SNPs (AllF) =  3913"
[1] "All rare fixed SNPs (AllFrare) =  780"
[1] "All fixed SNPs in recombinant regions (AllFrecomb) =  16"
[1] "All iSNPs (AllRI) =  4"
[1] "All rare  iSNPs (AllRIrare) =  0"
[1] "All iSNPs in recombinant regions (AllRIrecomb) =  0"
[1] "R is fixed, V only is intermediate, and rare (RonlyF_VIrare) =  0"
[1] "R is fixed, C only is intermediate, and rare (RonlyF_CIrare) =  0"
[1] "R is fixed, V and C are intermediate, and rare (RonlyF_CandVIrare) =  0"
[1] "C is fixed, V only is intermediate, and rare (ConlyF_VIrare) =  0"
[1] "C is fixed, R only is intermediate, and rare (ConlyF_RIrare) =  0"
[1] "C is fixed, R and V are intermediate, and rare (ConlyF_RandVIrare) =  0"
[1] "V is fixed, C only is intermediate, and rare (VonlyF_CIrare) =  0"
[1] "V is fixed, R only is intermediate, and rare (VonlyF_RIrare) =  0"
[1] "V is fixed, R and C are intermediate, and rare (VonlyF_CandRIrare) =  0"
[1] "R and C are fixed, V is intermediate, and rare (RCF_VIrare) =  0"
[1] "R and V are fixed, C is intermediate, and rare (RVF_CIrare) =  0"
[1] "V and C are fixed, R is intermediate, and rare (CVF_RIrare) =  0"

Warning: Removed 38 rows containing missing values (geom_point).
Warning: Removed 384 rows containing missing values (geom_point).
Warning: Removed 5 rows containing missing values (geom_point).
Warning: Removed 427 rows containing non-finite values (stat_boxplot).

[1] "Number cDenovo Ref SNPs for C =  334"
[1] "Number cDenovo Non-Ref SNPs for C =  1498"
[1] "Number cDenovo iSNPs for C =  0"
[1] "Number cDenovo Ref SNPs for R =  283"
[1] "Number cDenovo Non-Ref SNPs for R =  1202"
[1] "Number cDenovo iSNPs for R =  1"
[1] "Number cDenovo Ref SNPs for V =  342"
[1] "Number cDenovo Non-Ref SNPs for V =  1523"
[1] "Number cDenovo iSNPs for V =  0"
[[1]]

[[2]]

[[3]]

[[4]]

[[5]]

[[6]]

[[7]]

[[8]]

[[9]]

Subject 564

SNP_analysis_pipeline(subject_id = 564)

[1] "SUBJECT_ID is 564"
[1] "Rare iSNP cutoff =  3"
[1] "num rare iSNPs =  4383"
[1] "num common iSNPs =  4970"
[1] "Recombination block cutoff = 3"
[1] "Num bases in C recomb blocks=  0"
[1] "Num bases in R recomb = blocks 23231"
[1] "Num bases in V recomb = blocks 23231"
[1] "Coverage cutoff =  10"
[1] "Numbers of R bases above cutoff is  1035161"
[1] "Numbers of C bases above cutoff is  1030082"
[1] "Numbers of V bases above cutoff is  1013781"
[1] "Number of iSNP positions =  5253"
[1] "R only fixed SNPs (RonlyF) =  0"
[1] "R only rare fixed SNPs (RonlyFrare) =  0"
[1] "R only fixed SNPs in recombinant regions (RonlyFrecomb) =  0"
[1] "R only iSNPs (RonlyRI) =  0"
[1] "R only rare iSNPs (RonlyRIrare) =  0"
[1] "R only iSNPs in recombinant regions (RonlyRIrecomb) =  0"
[1] "C only fixed SNPs (ConlyF) =  231"
[1] "C only rare fixed SNPs (ConlyFrare) =  57"
[1] "C only fixed SNPs in recombinant regions (ConlyFrecomb) =  101"
[1] "C only iSNPs (ConlyRI) =  4"
[1] "C only rare iSNPs (ConlyRIrare) =  4"
[1] "C only iSNPs in recombinant regions (ConlyRIrecomb) =  0"
[1] "V only fixed SNPs (VonlyF) =  0"
[1] "V only rare fixed SNPs (VonlyFrare) =  0"
[1] "V only fixed SNPs in recombinant regions (VonlyFrecombb) =  0"
[1] "V only iSNPs (VonlyRI) =  58"
[1] "V only rare iSNPs (VonlyRIrare) =  53"
[1] "V only iSNPs in recombinant regions (VonlyRIrecomb) =  1"
[1] "RC only fixed SNPs (RConlyF) =  0"
[1] "RC only rare fixed SNPs (RConlyFrare) =  0"
[1] "RC only fixed SNPs in recombinant regions (RConlyFrecomb) =  0"
[1] "RC only iSNPs (RConlyRI) =  0"
[1] "RC only rare iSNPs (RConlyRIrare) =  0"
[1] "RC only iSNPs in recombinant regions (RConlyRIrecomb) =  0"
[1] "RV only fixed SNPs (RVonlyF) =  179"
[1] "RV only rare fixed SNPs (RVonlyFrare) =  96"
[1] "RV only fixed SNPs in recombinant regions (RVonlyFrecomb) =  58"
[1] "RV only iSNPs (RVonlyRI) =  1"
[1] "RV only rare iSNPs (RVonlyRIrare) =  1"
[1] "RV only iSNPs in recombinant regions (RVonlyRIrecomb) =  0"
[1] "VC only fixed SNPs (VConlyF) =  0"
[1] "VC only rare fixed SNPs (VConlyFrare) =  0"
[1] "VC only fixed SNPs in recombinant regions (VConlyFrecomb) =  0"
[1] "VC only iSNPs (VConlyRI) =  0"
[1] "VC only rare iSNPs (VConlyRIrare) =  0"
[1] "VC only iSNPs in recombinant regions (VConlyRIrecomb) =  0"
[1] "All fixed SNPs (AllF) =  4668"
[1] "All rare fixed SNPs (AllFrare) =  881"
[1] "All fixed SNPs in recombinant regions (AllFrecomb) =  20"
[1] "All iSNPs (AllRI) =  7"
[1] "All rare  iSNPs (AllRIrare) =  0"
[1] "All iSNPs in recombinant regions (AllRIrecomb) =  0"
[1] "R is fixed, V only is intermediate, and rare (RonlyF_VIrare) =  0"
[1] "R is fixed, C only is intermediate, and rare (RonlyF_CIrare) =  0"
[1] "R is fixed, V and C are intermediate, and rare (RonlyF_CandVIrare) =  0"
[1] "C is fixed, V only is intermediate, and rare (ConlyF_VIrare) =  0"
[1] "C is fixed, R only is intermediate, and rare (ConlyF_RIrare) =  0"
[1] "C is fixed, R and V are intermediate, and rare (ConlyF_RandVIrare) =  0"
[1] "V is fixed, C only is intermediate, and rare (VonlyF_CIrare) =  0"
[1] "V is fixed, R only is intermediate, and rare (VonlyF_RIrare) =  0"
[1] "V is fixed, R and C are intermediate, and rare (VonlyF_CandRIrare) =  0"
[1] "R and C are fixed, V is intermediate, and rare (RCF_VIrare) =  1"
[1] "R and V are fixed, C is intermediate, and rare (RVF_CIrare) =  0"
[1] "V and C are fixed, R is intermediate, and rare (CVF_RIrare) =  0"

Warning: Removed 20 rows containing missing values (geom_point).
Warning: Removed 2 rows containing missing values (geom_point).
Warning: Removed 39 rows containing missing values (geom_point).
Warning: Removed 61 rows containing non-finite values (stat_boxplot).

[1] "Number cDenovo Ref SNPs for C =  338"
[1] "Number cDenovo Non-Ref SNPs for C =  1513"
[1] "Number cDenovo iSNPs for C =  0"
[1] "Number cDenovo Ref SNPs for R =  344"
[1] "Number cDenovo Non-Ref SNPs for R =  1524"
[1] "Number cDenovo iSNPs for R =  1"
[1] "Number cDenovo Ref SNPs for V =  332"
[1] "Number cDenovo Non-Ref SNPs for V =  1475"
[1] "Number cDenovo iSNPs for V =  25"
[[1]]

[[2]]

[[3]]

[[4]]

[[5]]

[[6]]

[[7]]

[[8]]

[[9]]

Subject 753

SNP_analysis_pipeline(subject_id = 753)

[1] "SUBJECT_ID is 753"
[1] "Rare iSNP cutoff =  3"
[1] "num rare iSNPs =  4383"
[1] "num common iSNPs =  4970"
[1] "Recombination block cutoff = 3"
[1] "Num bases in C recomb blocks=  0"
[1] "Num bases in R recomb = blocks 0"
[1] "Num bases in V recomb = blocks 0"
[1] "Coverage cutoff =  10"
[1] "Numbers of R bases above cutoff is  619998"
[1] "Numbers of C bases above cutoff is  1037605"
[1] "Numbers of V bases above cutoff is  1037470"
[1] "Number of iSNP positions =  912"
[1] "R only fixed SNPs (RonlyF) =  0"
[1] "R only rare fixed SNPs (RonlyFrare) =  0"
[1] "R only fixed SNPs in recombinant regions (RonlyFrecomb) =  0"
[1] "R only iSNPs (RonlyRI) =  233"
[1] "R only rare iSNPs (RonlyRIrare) =  105"
[1] "R only iSNPs in recombinant regions (RonlyRIrecomb) =  0"
[1] "C only fixed SNPs (ConlyF) =  0"
[1] "C only rare fixed SNPs (ConlyFrare) =  0"
[1] "C only fixed SNPs in recombinant regions (ConlyFrecomb) =  0"
[1] "C only iSNPs (ConlyRI) =  1"
[1] "C only rare iSNPs (ConlyRIrare) =  1"
[1] "C only iSNPs in recombinant regions (ConlyRIrecomb) =  0"
[1] "V only fixed SNPs (VonlyF) =  0"
[1] "V only rare fixed SNPs (VonlyFrare) =  0"
[1] "V only fixed SNPs in recombinant regions (VonlyFrecombb) =  0"
[1] "V only iSNPs (VonlyRI) =  0"
[1] "V only rare iSNPs (VonlyRIrare) =  0"
[1] "V only iSNPs in recombinant regions (VonlyRIrecomb) =  0"
[1] "RC only fixed SNPs (RConlyF) =  0"
[1] "RC only rare fixed SNPs (RConlyFrare) =  0"
[1] "RC only fixed SNPs in recombinant regions (RConlyFrecomb) =  0"
[1] "RC only iSNPs (RConlyRI) =  1"
[1] "RC only rare iSNPs (RConlyRIrare) =  0"
[1] "RC only iSNPs in recombinant regions (RConlyRIrecomb) =  0"
[1] "RV only fixed SNPs (RVonlyF) =  0"
[1] "RV only rare fixed SNPs (RVonlyFrare) =  0"
[1] "RV only fixed SNPs in recombinant regions (RVonlyFrecomb) =  0"
[1] "RV only iSNPs (RVonlyRI) =  0"
[1] "RV only rare iSNPs (RVonlyRIrare) =  0"
[1] "RV only iSNPs in recombinant regions (RVonlyRIrecomb) =  0"
[1] "VC only fixed SNPs (VConlyF) =  0"
[1] "VC only rare fixed SNPs (VConlyFrare) =  0"
[1] "VC only fixed SNPs in recombinant regions (VConlyFrecomb) =  0"
[1] "VC only iSNPs (VConlyRI) =  2"
[1] "VC only rare iSNPs (VConlyRIrare) =  0"
[1] "VC only iSNPs in recombinant regions (VConlyRIrecomb) =  0"
[1] "All fixed SNPs (AllF) =  623"
[1] "All rare fixed SNPs (AllFrare) =  426"
[1] "All fixed SNPs in recombinant regions (AllFrecomb) =  0"
[1] "All iSNPs (AllRI) =  6"
[1] "All rare  iSNPs (AllRIrare) =  2"
[1] "All iSNPs in recombinant regions (AllRIrecomb) =  0"
[1] "R is fixed, V only is intermediate, and rare (RonlyF_VIrare) =  0"
[1] "R is fixed, C only is intermediate, and rare (RonlyF_CIrare) =  0"
[1] "R is fixed, V and C are intermediate, and rare (RonlyF_CandVIrare) =  0"
[1] "C is fixed, V only is intermediate, and rare (ConlyF_VIrare) =  0"
[1] "C is fixed, R only is intermediate, and rare (ConlyF_RIrare) =  0"
[1] "C is fixed, R and V are intermediate, and rare (ConlyF_RandVIrare) =  0"
[1] "V is fixed, C only is intermediate, and rare (VonlyF_CIrare) =  0"
[1] "V is fixed, R only is intermediate, and rare (VonlyF_RIrare) =  0"
[1] "V is fixed, R and C are intermediate, and rare (VonlyF_CandRIrare) =  0"
[1] "R and C are fixed, V is intermediate, and rare (RCF_VIrare) =  0"
[1] "R and V are fixed, C is intermediate, and rare (RVF_CIrare) =  0"
[1] "V and C are fixed, R is intermediate, and rare (CVF_RIrare) =  9"

Warning: Removed 4 rows containing missing values (geom_point).
Warning: Removed 771 rows containing missing values (geom_point).
Warning: Removed 6 rows containing missing values (geom_point).
Warning: Removed 781 rows containing non-finite values (stat_boxplot).

[1] "Number cDenovo Ref SNPs for C =  1609"
[1] "Number cDenovo Non-Ref SNPs for C =  259"
[1] "Number cDenovo iSNPs for C =  0"
[1] "Number cDenovo Ref SNPs for R =  926"
[1] "Number cDenovo Non-Ref SNPs for R =  143"
[1] "Number cDenovo iSNPs for R =  32"
[1] "Number cDenovo Ref SNPs for V =  1608"
[1] "Number cDenovo Non-Ref SNPs for V =  258"
[1] "Number cDenovo iSNPs for V =  0"
[[1]]

[[2]]

[[3]]

[[4]]

[[5]]

[[6]]

[[7]]

[[8]]

[[9]]

Subject 908

SNP_analysis_pipeline(subject_id = 908)

[1] "SUBJECT_ID is 908"
[1] "Rare iSNP cutoff =  3"
[1] "num rare iSNPs =  4383"
[1] "num common iSNPs =  4970"
[1] "Recombination block cutoff = 3"
[1] "Num bases in C recomb blocks=  1485"
[1] "Num bases in R recomb = blocks 1691"
[1] "Num bases in V recomb = blocks 1485"
[1] "Coverage cutoff =  10"
[1] "Numbers of R bases above cutoff is  1033470"
[1] "Numbers of C bases above cutoff is  1032274"
[1] "Numbers of V bases above cutoff is  1006412"
[1] "Number of iSNP positions =  5112"
[1] "R only fixed SNPs (RonlyF) =  0"
[1] "R only rare fixed SNPs (RonlyFrare) =  0"
[1] "R only fixed SNPs in recombinant regions (RonlyFrecomb) =  0"
[1] "R only iSNPs (RonlyRI) =  0"
[1] "R only rare iSNPs (RonlyRIrare) =  0"
[1] "R only iSNPs in recombinant regions (RonlyRIrecomb) =  0"
[1] "C only fixed SNPs (ConlyF) =  0"
[1] "C only rare fixed SNPs (ConlyFrare) =  0"
[1] "C only fixed SNPs in recombinant regions (ConlyFrecomb) =  0"
[1] "C only iSNPs (ConlyRI) =  15"
[1] "C only rare iSNPs (ConlyRIrare) =  6"
[1] "C only iSNPs in recombinant regions (ConlyRIrecomb) =  0"
[1] "V only fixed SNPs (VonlyF) =  0"
[1] "V only rare fixed SNPs (VonlyFrare) =  0"
[1] "V only fixed SNPs in recombinant regions (VonlyFrecombb) =  0"
[1] "V only iSNPs (VonlyRI) =  86"
[1] "V only rare iSNPs (VonlyRIrare) =  80"
[1] "V only iSNPs in recombinant regions (VonlyRIrecomb) =  0"
[1] "RC only fixed SNPs (RConlyF) =  0"
[1] "RC only rare fixed SNPs (RConlyFrare) =  0"
[1] "RC only fixed SNPs in recombinant regions (RConlyFrecomb) =  0"
[1] "RC only iSNPs (RConlyRI) =  2"
[1] "RC only rare iSNPs (RConlyRIrare) =  0"
[1] "RC only iSNPs in recombinant regions (RConlyRIrecomb) =  0"
[1] "RV only fixed SNPs (RVonlyF) =  0"
[1] "RV only rare fixed SNPs (RVonlyFrare) =  0"
[1] "RV only fixed SNPs in recombinant regions (RVonlyFrecomb) =  0"
[1] "RV only iSNPs (RVonlyRI) =  1"
[1] "RV only rare iSNPs (RVonlyRIrare) =  0"
[1] "RV only iSNPs in recombinant regions (RVonlyRIrecomb) =  0"
[1] "VC only fixed SNPs (VConlyF) =  0"
[1] "VC only rare fixed SNPs (VConlyFrare) =  0"
[1] "VC only fixed SNPs in recombinant regions (VConlyFrecomb) =  0"
[1] "VC only iSNPs (VConlyRI) =  0"
[1] "VC only rare iSNPs (VConlyRIrare) =  0"
[1] "VC only iSNPs in recombinant regions (VConlyRIrecomb) =  0"
[1] "All fixed SNPs (AllF) =  4852"
[1] "All rare fixed SNPs (AllFrare) =  928"
[1] "All fixed SNPs in recombinant regions (AllFrecomb) =  35"
[1] "All iSNPs (AllRI) =  6"
[1] "All rare  iSNPs (AllRIrare) =  0"
[1] "All iSNPs in recombinant regions (AllRIrecomb) =  0"
[1] "R is fixed, V only is intermediate, and rare (RonlyF_VIrare) =  0"
[1] "R is fixed, C only is intermediate, and rare (RonlyF_CIrare) =  0"
[1] "R is fixed, V and C are intermediate, and rare (RonlyF_CandVIrare) =  0"
[1] "C is fixed, V only is intermediate, and rare (ConlyF_VIrare) =  0"
[1] "C is fixed, R only is intermediate, and rare (ConlyF_RIrare) =  0"
[1] "C is fixed, R and V are intermediate, and rare (ConlyF_RandVIrare) =  0"
[1] "V is fixed, C only is intermediate, and rare (VonlyF_CIrare) =  0"
[1] "V is fixed, R only is intermediate, and rare (VonlyF_RIrare) =  0"
[1] "V is fixed, R and C are intermediate, and rare (VonlyF_CandRIrare) =  0"
[1] "R and C are fixed, V is intermediate, and rare (RCF_VIrare) =  5"
[1] "R and V are fixed, C is intermediate, and rare (RVF_CIrare) =  0"
[1] "V and C are fixed, R is intermediate, and rare (CVF_RIrare) =  0"

Warning: Removed 5 rows containing missing values (geom_point).
Warning: Removed 8 rows containing missing values (geom_point).
Warning: Removed 65 rows containing missing values (geom_point).
Warning: Removed 78 rows containing non-finite values (stat_boxplot).

[1] "Number cDenovo Ref SNPs for C =  340"
[1] "Number cDenovo Non-Ref SNPs for C =  1526"
[1] "Number cDenovo iSNPs for C =  0"
[1] "Number cDenovo Ref SNPs for R =  340"
[1] "Number cDenovo Non-Ref SNPs for R =  1523"
[1] "Number cDenovo iSNPs for R =  0"
[1] "Number cDenovo Ref SNPs for V =  329"
[1] "Number cDenovo Non-Ref SNPs for V =  1450"
[1] "Number cDenovo iSNPs for V =  27"
[[1]]

[[2]]

[[3]]

[[4]]

[[5]]

[[6]]

[[7]]

[[8]]

[[9]]

Subject 927

SNP_analysis_pipeline(subject_id = 927)

[1] "SUBJECT_ID is 927"
[1] "Rare iSNP cutoff =  3"
[1] "num rare iSNPs =  4383"
[1] "num common iSNPs =  4970"
[1] "Recombination block cutoff = 3"
[1] "Num bases in C recomb blocks=  27215"
[1] "Num bases in R recomb = blocks 27215"
[1] "Num bases in V recomb = blocks 8664"
[1] "Coverage cutoff =  10"
[1] "Numbers of R bases above cutoff is  1026496"
[1] "Numbers of C bases above cutoff is  1034845"
[1] "Numbers of V bases above cutoff is  1034464"
[1] "Number of iSNP positions =  5283"
[1] "R only fixed SNPs (RonlyF) =  0"
[1] "R only rare fixed SNPs (RonlyFrare) =  0"
[1] "R only fixed SNPs in recombinant regions (RonlyFrecomb) =  0"
[1] "R only iSNPs (RonlyRI) =  2"
[1] "R only rare iSNPs (RonlyRIrare) =  0"
[1] "R only iSNPs in recombinant regions (RonlyRIrecomb) =  0"
[1] "C only fixed SNPs (ConlyF) =  0"
[1] "C only rare fixed SNPs (ConlyFrare) =  0"
[1] "C only fixed SNPs in recombinant regions (ConlyFrecomb) =  0"
[1] "C only iSNPs (ConlyRI) =  0"
[1] "C only rare iSNPs (ConlyRIrare) =  0"
[1] "C only iSNPs in recombinant regions (ConlyRIrecomb) =  0"
[1] "V only fixed SNPs (VonlyF) =  0"
[1] "V only rare fixed SNPs (VonlyFrare) =  0"
[1] "V only fixed SNPs in recombinant regions (VonlyFrecombb) =  0"
[1] "V only iSNPs (VonlyRI) =  4"
[1] "V only rare iSNPs (VonlyRIrare) =  0"
[1] "V only iSNPs in recombinant regions (VonlyRIrecomb) =  1"
[1] "RC only fixed SNPs (RConlyF) =  0"
[1] "RC only rare fixed SNPs (RConlyFrare) =  0"
[1] "RC only fixed SNPs in recombinant regions (RConlyFrecomb) =  0"
[1] "RC only iSNPs (RConlyRI) =  1"
[1] "RC only rare iSNPs (RConlyRIrare) =  0"
[1] "RC only iSNPs in recombinant regions (RConlyRIrecomb) =  0"
[1] "RV only fixed SNPs (RVonlyF) =  0"
[1] "RV only rare fixed SNPs (RVonlyFrare) =  0"
[1] "RV only fixed SNPs in recombinant regions (RVonlyFrecomb) =  0"
[1] "RV only iSNPs (RVonlyRI) =  1"
[1] "RV only rare iSNPs (RVonlyRIrare) =  0"
[1] "RV only iSNPs in recombinant regions (RVonlyRIrecomb) =  1"
[1] "VC only fixed SNPs (VConlyF) =  0"
[1] "VC only rare fixed SNPs (VConlyFrare) =  0"
[1] "VC only fixed SNPs in recombinant regions (VConlyFrecomb) =  0"
[1] "VC only iSNPs (VConlyRI) =  0"
[1] "VC only rare iSNPs (VConlyRIrare) =  0"
[1] "VC only iSNPs in recombinant regions (VConlyRIrecomb) =  0"
[1] "All fixed SNPs (AllF) =  5244"
[1] "All rare fixed SNPs (AllFrare) =  1247"
[1] "All fixed SNPs in recombinant regions (AllFrecomb) =  142"
[1] "All iSNPs (AllRI) =  24"
[1] "All rare  iSNPs (AllRIrare) =  0"
[1] "All iSNPs in recombinant regions (AllRIrecomb) =  2"
[1] "R is fixed, V only is intermediate, and rare (RonlyF_VIrare) =  0"
[1] "R is fixed, C only is intermediate, and rare (RonlyF_CIrare) =  0"
[1] "R is fixed, V and C are intermediate, and rare (RonlyF_CandVIrare) =  0"
[1] "C is fixed, V only is intermediate, and rare (ConlyF_VIrare) =  0"
[1] "C is fixed, R only is intermediate, and rare (ConlyF_RIrare) =  0"
[1] "C is fixed, R and V are intermediate, and rare (ConlyF_RandVIrare) =  0"
[1] "V is fixed, C only is intermediate, and rare (VonlyF_CIrare) =  0"
[1] "V is fixed, R only is intermediate, and rare (VonlyF_RIrare) =  0"
[1] "V is fixed, R and C are intermediate, and rare (VonlyF_CandRIrare) =  0"
[1] "R and C are fixed, V is intermediate, and rare (RCF_VIrare) =  0"
[1] "R and V are fixed, C is intermediate, and rare (RVF_CIrare) =  0"
[1] "V and C are fixed, R is intermediate, and rare (CVF_RIrare) =  1"

Warning: Removed 11 rows containing missing values (geom_point).
Warning: Removed 25 rows containing missing values (geom_point).
Warning: Removed 12 rows containing missing values (geom_point).
Warning: Removed 48 rows containing non-finite values (stat_boxplot).

[1] "Number cDenovo Ref SNPs for C =  328"
[1] "Number cDenovo Non-Ref SNPs for C =  1529"
[1] "Number cDenovo iSNPs for C =  0"
[1] "Number cDenovo Ref SNPs for R =  323"
[1] "Number cDenovo Non-Ref SNPs for R =  1520"
[1] "Number cDenovo iSNPs for R =  0"
[1] "Number cDenovo Ref SNPs for V =  326"
[1] "Number cDenovo Non-Ref SNPs for V =  1530"
[1] "Number cDenovo iSNPs for V =  0"
[[1]]

[[2]]

[[3]]

[[4]]

[[5]]

[[6]]

[[7]]

[[8]]

[[9]]

Subject 951

SNP_analysis_pipeline(subject_id = 951)

[1] "SUBJECT_ID is 951"
[1] "Rare iSNP cutoff =  3"
[1] "num rare iSNPs =  4383"
[1] "num common iSNPs =  4970"
[1] "Recombination block cutoff = 3"
[1] "Num bases in C recomb blocks=  13256"
[1] "Num bases in R recomb = blocks 16904"
[1] "Num bases in V recomb = blocks 13256"
[1] "Coverage cutoff =  10"
[1] "Numbers of R bases above cutoff is  1013234"
[1] "Numbers of C bases above cutoff is  1035195"
[1] "Numbers of V bases above cutoff is  1035300"
[1] "Number of iSNP positions =  5191"
[1] "R only fixed SNPs (RonlyF) =  0"
[1] "R only rare fixed SNPs (RonlyFrare) =  0"
[1] "R only fixed SNPs in recombinant regions (RonlyFrecomb) =  0"
[1] "R only iSNPs (RonlyRI) =  14"
[1] "R only rare iSNPs (RonlyRIrare) =  2"
[1] "R only iSNPs in recombinant regions (RonlyRIrecomb) =  0"
[1] "C only fixed SNPs (ConlyF) =  0"
[1] "C only rare fixed SNPs (ConlyFrare) =  0"
[1] "C only fixed SNPs in recombinant regions (ConlyFrecomb) =  0"
[1] "C only iSNPs (ConlyRI) =  2"
[1] "C only rare iSNPs (ConlyRIrare) =  1"
[1] "C only iSNPs in recombinant regions (ConlyRIrecomb) =  0"
[1] "V only fixed SNPs (VonlyF) =  0"
[1] "V only rare fixed SNPs (VonlyFrare) =  0"
[1] "V only fixed SNPs in recombinant regions (VonlyFrecombb) =  0"
[1] "V only iSNPs (VonlyRI) =  8"
[1] "V only rare iSNPs (VonlyRIrare) =  1"
[1] "V only iSNPs in recombinant regions (VonlyRIrecomb) =  0"
[1] "RC only fixed SNPs (RConlyF) =  0"
[1] "RC only rare fixed SNPs (RConlyFrare) =  0"
[1] "RC only fixed SNPs in recombinant regions (RConlyFrecomb) =  0"
[1] "RC only iSNPs (RConlyRI) =  1"
[1] "RC only rare iSNPs (RConlyRIrare) =  0"
[1] "RC only iSNPs in recombinant regions (RConlyRIrecomb) =  0"
[1] "RV only fixed SNPs (RVonlyF) =  0"
[1] "RV only rare fixed SNPs (RVonlyFrare) =  0"
[1] "RV only fixed SNPs in recombinant regions (RVonlyFrecomb) =  0"
[1] "RV only iSNPs (RVonlyRI) =  0"
[1] "RV only rare iSNPs (RVonlyRIrare) =  0"
[1] "RV only iSNPs in recombinant regions (RVonlyRIrecomb) =  0"
[1] "VC only fixed SNPs (VConlyF) =  0"
[1] "VC only rare fixed SNPs (VConlyFrare) =  0"
[1] "VC only fixed SNPs in recombinant regions (VConlyFrecomb) =  0"
[1] "VC only iSNPs (VConlyRI) =  2"
[1] "VC only rare iSNPs (VConlyRIrare) =  2"
[1] "VC only iSNPs in recombinant regions (VConlyRIrecomb) =  0"
[1] "All fixed SNPs (AllF) =  5069"
[1] "All rare fixed SNPs (AllFrare) =  1083"
[1] "All fixed SNPs in recombinant regions (AllFrecomb) =  84"
[1] "All iSNPs (AllRI) =  17"
[1] "All rare  iSNPs (AllRIrare) =  0"
[1] "All iSNPs in recombinant regions (AllRIrecomb) =  0"
[1] "R is fixed, V only is intermediate, and rare (RonlyF_VIrare) =  0"
[1] "R is fixed, C only is intermediate, and rare (RonlyF_CIrare) =  0"
[1] "R is fixed, V and C are intermediate, and rare (RonlyF_CandVIrare) =  0"
[1] "C is fixed, V only is intermediate, and rare (ConlyF_VIrare) =  0"
[1] "C is fixed, R only is intermediate, and rare (ConlyF_RIrare) =  0"
[1] "C is fixed, R and V are intermediate, and rare (ConlyF_RandVIrare) =  4"
[1] "V is fixed, C only is intermediate, and rare (VonlyF_CIrare) =  0"
[1] "V is fixed, R only is intermediate, and rare (VonlyF_RIrare) =  0"
[1] "V is fixed, R and C are intermediate, and rare (VonlyF_CandRIrare) =  0"
[1] "R and C are fixed, V is intermediate, and rare (RCF_VIrare) =  18"
[1] "R and V are fixed, C is intermediate, and rare (RVF_CIrare) =  0"
[1] "V and C are fixed, R is intermediate, and rare (CVF_RIrare) =  0"

Warning: Removed 4 rows containing missing values (geom_point).
Warning: Removed 63 rows containing missing values (geom_point).
Warning: Removed 9 rows containing missing values (geom_point).
Warning: Removed 76 rows containing non-finite values (stat_boxplot).

[1] "Number cDenovo Ref SNPs for C =  334"
[1] "Number cDenovo Non-Ref SNPs for C =  1533"
[1] "Number cDenovo iSNPs for C =  0"
[1] "Number cDenovo Ref SNPs for R =  323"
[1] "Number cDenovo Non-Ref SNPs for R =  1485"
[1] "Number cDenovo iSNPs for R =  0"
[1] "Number cDenovo Ref SNPs for V =  333"
[1] "Number cDenovo Non-Ref SNPs for V =  1528"
[1] "Number cDenovo iSNPs for V =  1"
[[1]]

[[2]]

[[3]]

[[4]]

[[5]]

[[6]]

[[7]]

[[8]]

[[9]]

Subject 968

SNP_analysis_pipeline(subject_id = 968)

[1] "SUBJECT_ID is 968"
[1] "Rare iSNP cutoff =  3"
[1] "num rare iSNPs =  4383"
[1] "num common iSNPs =  4970"
[1] "Recombination block cutoff = 3"
[1] "Num bases in C recomb blocks=  0"
[1] "Num bases in R recomb = blocks 0"
[1] "Num bases in V recomb = blocks 0"
[1] "Coverage cutoff =  10"
[1] "Numbers of R bases above cutoff is  578500"
[1] "Numbers of C bases above cutoff is  1029349"
[1] "Numbers of V bases above cutoff is  1037840"
[1] "Number of iSNP positions =  1245"
[1] "R only fixed SNPs (RonlyF) =  0"
[1] "R only rare fixed SNPs (RonlyFrare) =  0"
[1] "R only fixed SNPs in recombinant regions (RonlyFrecomb) =  0"
[1] "R only iSNPs (RonlyRI) =  537"
[1] "R only rare iSNPs (RonlyRIrare) =  114"
[1] "R only iSNPs in recombinant regions (RonlyRIrecomb) =  0"
[1] "C only fixed SNPs (ConlyF) =  0"
[1] "C only rare fixed SNPs (ConlyFrare) =  0"
[1] "C only fixed SNPs in recombinant regions (ConlyFrecomb) =  0"
[1] "C only iSNPs (ConlyRI) =  2"
[1] "C only rare iSNPs (ConlyRIrare) =  1"
[1] "C only iSNPs in recombinant regions (ConlyRIrecomb) =  0"
[1] "V only fixed SNPs (VonlyF) =  0"
[1] "V only rare fixed SNPs (VonlyFrare) =  0"
[1] "V only fixed SNPs in recombinant regions (VonlyFrecombb) =  0"
[1] "V only iSNPs (VonlyRI) =  0"
[1] "V only rare iSNPs (VonlyRIrare) =  0"
[1] "V only iSNPs in recombinant regions (VonlyRIrecomb) =  0"
[1] "RC only fixed SNPs (RConlyF) =  0"
[1] "RC only rare fixed SNPs (RConlyFrare) =  0"
[1] "RC only fixed SNPs in recombinant regions (RConlyFrecomb) =  0"
[1] "RC only iSNPs (RConlyRI) =  0"
[1] "RC only rare iSNPs (RConlyRIrare) =  0"
[1] "RC only iSNPs in recombinant regions (RConlyRIrecomb) =  0"
[1] "RV only fixed SNPs (RVonlyF) =  0"
[1] "RV only rare fixed SNPs (RVonlyFrare) =  0"
[1] "RV only fixed SNPs in recombinant regions (RVonlyFrecomb) =  0"
[1] "RV only iSNPs (RVonlyRI) =  0"
[1] "RV only rare iSNPs (RVonlyRIrare) =  0"
[1] "RV only iSNPs in recombinant regions (RVonlyRIrecomb) =  0"
[1] "VC only fixed SNPs (VConlyF) =  0"
[1] "VC only rare fixed SNPs (VConlyFrare) =  0"
[1] "VC only fixed SNPs in recombinant regions (VConlyFrecomb) =  0"
[1] "VC only iSNPs (VConlyRI) =  1"
[1] "VC only rare iSNPs (VConlyRIrare) =  1"
[1] "VC only iSNPs in recombinant regions (VConlyRIrecomb) =  0"
[1] "All fixed SNPs (AllF) =  586"
[1] "All rare fixed SNPs (AllFrare) =  403"
[1] "All fixed SNPs in recombinant regions (AllFrecomb) =  0"
[1] "All iSNPs (AllRI) =  9"
[1] "All rare  iSNPs (AllRIrare) =  0"
[1] "All iSNPs in recombinant regions (AllRIrecomb) =  0"
[1] "R is fixed, V only is intermediate, and rare (RonlyF_VIrare) =  0"
[1] "R is fixed, C only is intermediate, and rare (RonlyF_CIrare) =  0"
[1] "R is fixed, V and C are intermediate, and rare (RonlyF_CandVIrare) =  0"
[1] "C is fixed, V only is intermediate, and rare (ConlyF_VIrare) =  0"
[1] "C is fixed, R only is intermediate, and rare (ConlyF_RIrare) =  0"
[1] "C is fixed, R and V are intermediate, and rare (ConlyF_RandVIrare) =  0"
[1] "V is fixed, C only is intermediate, and rare (VonlyF_CIrare) =  0"
[1] "V is fixed, R only is intermediate, and rare (VonlyF_RIrare) =  0"
[1] "V is fixed, R and C are intermediate, and rare (VonlyF_CandRIrare) =  0"
[1] "R and C are fixed, V is intermediate, and rare (RCF_VIrare) =  0"
[1] "R and V are fixed, C is intermediate, and rare (RVF_CIrare) =  0"
[1] "V and C are fixed, R is intermediate, and rare (CVF_RIrare) =  19"

Warning: Removed 20 rows containing missing values (geom_point).
Warning: Removed 984 rows containing missing values (geom_point).
Warning: Removed 2 rows containing missing values (geom_point).
Warning: Removed 1006 rows containing non-finite values (stat_boxplot).

[1] "Number cDenovo Ref SNPs for C =  1607"
[1] "Number cDenovo Non-Ref SNPs for C =  244"
[1] "Number cDenovo iSNPs for C =  0"
[1] "Number cDenovo Ref SNPs for R =  671"
[1] "Number cDenovo Non-Ref SNPs for R =  84"
[1] "Number cDenovo iSNPs for R =  132"
[1] "Number cDenovo Ref SNPs for V =  1623"
[1] "Number cDenovo Non-Ref SNPs for V =  246"
[1] "Number cDenovo iSNPs for V =  0"
[[1]]

[[2]]

[[3]]

[[4]]

[[5]]

[[6]]

[[7]]

[[8]]

[[9]]

Subject 1077

SNP_analysis_pipeline(subject_id = 1077)

[1] "SUBJECT_ID is 1077"
[1] "Rare iSNP cutoff =  3"
[1] "num rare iSNPs =  4383"
[1] "num common iSNPs =  4970"
[1] "Recombination block cutoff = 3"
[1] "Num bases in C recomb blocks=  15083"
[1] "Num bases in R recomb = blocks 14177"
[1] "Num bases in V recomb = blocks 14758"
[1] "Coverage cutoff =  10"
[1] "Numbers of R bases above cutoff is  798730"
[1] "Numbers of C bases above cutoff is  1036188"
[1] "Numbers of V bases above cutoff is  979111"
[1] "Number of iSNP positions =  3956"
[1] "R only fixed SNPs (RonlyF) =  0"
[1] "R only rare fixed SNPs (RonlyFrare) =  0"
[1] "R only fixed SNPs in recombinant regions (RonlyFrecomb) =  0"
[1] "R only iSNPs (RonlyRI) =  154"
[1] "R only rare iSNPs (RonlyRIrare) =  109"
[1] "R only iSNPs in recombinant regions (RonlyRIrecomb) =  4"
[1] "C only fixed SNPs (ConlyF) =  0"
[1] "C only rare fixed SNPs (ConlyFrare) =  0"
[1] "C only fixed SNPs in recombinant regions (ConlyFrecomb) =  0"
[1] "C only iSNPs (ConlyRI) =  0"
[1] "C only rare iSNPs (ConlyRIrare) =  0"
[1] "C only iSNPs in recombinant regions (ConlyRIrecomb) =  0"
[1] "V only fixed SNPs (VonlyF) =  0"
[1] "V only rare fixed SNPs (VonlyFrare) =  0"
[1] "V only fixed SNPs in recombinant regions (VonlyFrecombb) =  0"
[1] "V only iSNPs (VonlyRI) =  59"
[1] "V only rare iSNPs (VonlyRIrare) =  47"
[1] "V only iSNPs in recombinant regions (VonlyRIrecomb) =  1"
[1] "RC only fixed SNPs (RConlyF) =  0"
[1] "RC only rare fixed SNPs (RConlyFrare) =  0"
[1] "RC only fixed SNPs in recombinant regions (RConlyFrecomb) =  0"
[1] "RC only iSNPs (RConlyRI) =  2"
[1] "RC only rare iSNPs (RConlyRIrare) =  0"
[1] "RC only iSNPs in recombinant regions (RConlyRIrecomb) =  0"
[1] "RV only fixed SNPs (RVonlyF) =  0"
[1] "RV only rare fixed SNPs (RVonlyFrare) =  0"
[1] "RV only fixed SNPs in recombinant regions (RVonlyFrecomb) =  0"
[1] "RV only iSNPs (RVonlyRI) =  1"
[1] "RV only rare iSNPs (RVonlyRIrare) =  0"
[1] "RV only iSNPs in recombinant regions (RVonlyRIrecomb) =  0"
[1] "VC only fixed SNPs (VConlyF) =  0"
[1] "VC only rare fixed SNPs (VConlyFrare) =  0"
[1] "VC only fixed SNPs in recombinant regions (VConlyFrecomb) =  0"
[1] "VC only iSNPs (VConlyRI) =  0"
[1] "VC only rare iSNPs (VConlyRIrare) =  0"
[1] "VC only iSNPs in recombinant regions (VConlyRIrecomb) =  0"
[1] "All fixed SNPs (AllF) =  3145"
[1] "All rare fixed SNPs (AllFrare) =  620"
[1] "All fixed SNPs in recombinant regions (AllFrecomb) =  132"
[1] "All iSNPs (AllRI) =  6"
[1] "All rare  iSNPs (AllRIrare) =  0"
[1] "All iSNPs in recombinant regions (AllRIrecomb) =  0"
[1] "R is fixed, V only is intermediate, and rare (RonlyF_VIrare) =  0"
[1] "R is fixed, C only is intermediate, and rare (RonlyF_CIrare) =  0"
[1] "R is fixed, V and C are intermediate, and rare (RonlyF_CandVIrare) =  0"
[1] "C is fixed, V only is intermediate, and rare (ConlyF_VIrare) =  0"
[1] "C is fixed, R only is intermediate, and rare (ConlyF_RIrare) =  0"
[1] "C is fixed, R and V are intermediate, and rare (ConlyF_RandVIrare) =  0"
[1] "V is fixed, C only is intermediate, and rare (VonlyF_CIrare) =  0"
[1] "V is fixed, R only is intermediate, and rare (VonlyF_RIrare) =  0"
[1] "V is fixed, R and C are intermediate, and rare (VonlyF_CandRIrare) =  0"
[1] "R and C are fixed, V is intermediate, and rare (RCF_VIrare) =  2"
[1] "R and V are fixed, C is intermediate, and rare (RVF_CIrare) =  0"
[1] "V and C are fixed, R is intermediate, and rare (CVF_RIrare) =  26"

Warning: Removed 5 rows containing missing values (geom_point).
Warning: Removed 440 rows containing missing values (geom_point).
Warning: Removed 109 rows containing missing values (geom_point).
Warning: Removed 554 rows containing non-finite values (stat_boxplot).

[1] "Number cDenovo Ref SNPs for C =  338"
[1] "Number cDenovo Non-Ref SNPs for C =  1528"
[1] "Number cDenovo iSNPs for C =  0"
[1] "Number cDenovo Ref SNPs for R =  249"
[1] "Number cDenovo Non-Ref SNPs for R =  1053"
[1] "Number cDenovo iSNPs for R =  129"
[1] "Number cDenovo Ref SNPs for V =  315"
[1] "Number cDenovo Non-Ref SNPs for V =  1432"
[1] "Number cDenovo iSNPs for V =  15"
[[1]]

[[2]]

[[3]]

[[4]]

[[5]]

[[6]]

[[7]]

[[8]]

[[9]]

Subject 1078

SNP_analysis_pipeline(subject_id = 1078)

[1] "SUBJECT_ID is 1078"
[1] "Rare iSNP cutoff =  3"
[1] "num rare iSNPs =  4383"
[1] "num common iSNPs =  4970"
[1] "Recombination block cutoff = 3"
[1] "Num bases in C recomb blocks=  0"
[1] "Num bases in R recomb = blocks 22555"
[1] "Num bases in V recomb = blocks 35303"
[1] "Coverage cutoff =  10"
[1] "Numbers of R bases above cutoff is  875018"
[1] "Numbers of C bases above cutoff is  249618"
[1] "Numbers of V bases above cutoff is  1015869"
[1] "Number of iSNP positions =  1382"
[1] "R only fixed SNPs (RonlyF) =  96"
[1] "R only rare fixed SNPs (RonlyFrare) =  40"
[1] "R only fixed SNPs in recombinant regions (RonlyFrecomb) =  9"
[1] "R only iSNPs (RonlyRI) =  103"
[1] "R only rare iSNPs (RonlyRIrare) =  65"
[1] "R only iSNPs in recombinant regions (RonlyRIrecomb) =  20"
[1] "C only fixed SNPs (ConlyF) =  0"
[1] "C only rare fixed SNPs (ConlyFrare) =  0"
[1] "C only fixed SNPs in recombinant regions (ConlyFrecomb) =  0"
[1] "C only iSNPs (ConlyRI) =  85"
[1] "C only rare iSNPs (ConlyRIrare) =  74"
[1] "C only iSNPs in recombinant regions (ConlyRIrecomb) =  6"
[1] "V only fixed SNPs (VonlyF) =  1"
[1] "V only rare fixed SNPs (VonlyFrare) =  1"
[1] "V only fixed SNPs in recombinant regions (VonlyFrecombb) =  0"
[1] "V only iSNPs (VonlyRI) =  35"
[1] "V only rare iSNPs (VonlyRIrare) =  34"
[1] "V only iSNPs in recombinant regions (VonlyRIrecomb) =  1"
[1] "RC only fixed SNPs (RConlyF) =  1"
[1] "RC only rare fixed SNPs (RConlyFrare) =  0"
[1] "RC only fixed SNPs in recombinant regions (RConlyFrecomb) =  0"
[1] "RC only iSNPs (RConlyRI) =  33"
[1] "RC only rare iSNPs (RConlyRIrare) =  0"
[1] "RC only iSNPs in recombinant regions (RConlyRIrecomb) =  3"
[1] "RV only fixed SNPs (RVonlyF) =  0"
[1] "RV only rare fixed SNPs (RVonlyFrare) =  0"
[1] "RV only fixed SNPs in recombinant regions (RVonlyFrecomb) =  0"
[1] "RV only iSNPs (RVonlyRI) =  91"
[1] "RV only rare iSNPs (RVonlyRIrare) =  5"
[1] "RV only iSNPs in recombinant regions (RVonlyRIrecomb) =  25"
[1] "VC only fixed SNPs (VConlyF) =  4"
[1] "VC only rare fixed SNPs (VConlyFrare) =  2"
[1] "VC only fixed SNPs in recombinant regions (VConlyFrecomb) =  1"
[1] "VC only iSNPs (VConlyRI) =  17"
[1] "VC only rare iSNPs (VConlyRIrare) =  10"
[1] "VC only iSNPs in recombinant regions (VConlyRIrecomb) =  4"
[1] "All fixed SNPs (AllF) =  32"
[1] "All rare fixed SNPs (AllFrare) =  32"
[1] "All fixed SNPs in recombinant regions (AllFrecomb) =  8"
[1] "All iSNPs (AllRI) =  65"
[1] "All rare  iSNPs (AllRIrare) =  1"
[1] "All iSNPs in recombinant regions (AllRIrecomb) =  2"
[1] "R is fixed, V only is intermediate, and rare (RonlyF_VIrare) =  51"
[1] "R is fixed, C only is intermediate, and rare (RonlyF_CIrare) =  54"
[1] "R is fixed, V and C are intermediate, and rare (RonlyF_CandVIrare) =  58"
[1] "C is fixed, V only is intermediate, and rare (ConlyF_VIrare) =  8"
[1] "C is fixed, R only is intermediate, and rare (ConlyF_RIrare) =  0"
[1] "C is fixed, R and V are intermediate, and rare (ConlyF_RandVIrare) =  0"
[1] "V is fixed, C only is intermediate, and rare (VonlyF_CIrare) =  5"
[1] "V is fixed, R only is intermediate, and rare (VonlyF_RIrare) =  0"
[1] "V is fixed, R and C are intermediate, and rare (VonlyF_CandRIrare) =  0"
[1] "R and C are fixed, V is intermediate, and rare (RCF_VIrare) =  58"
[1] "R and V are fixed, C is intermediate, and rare (RVF_CIrare) =  58"
[1] "V and C are fixed, R is intermediate, and rare (CVF_RIrare) =  0"

Warning: Removed 1332 rows containing missing values (geom_point).
Warning: Removed 256 rows containing missing values (geom_point).
Warning: Removed 23 rows containing missing values (geom_point).
Warning: Removed 1611 rows containing non-finite values (stat_boxplot).

[1] "Number cDenovo Ref SNPs for C =  279"
[1] "Number cDenovo Non-Ref SNPs for C =  21"
[1] "Number cDenovo iSNPs for C =  234"
[1] "Number cDenovo Ref SNPs for R =  265"
[1] "Number cDenovo Non-Ref SNPs for R =  1164"
[1] "Number cDenovo iSNPs for R =  181"
[1] "Number cDenovo Ref SNPs for V =  624"
[1] "Number cDenovo Non-Ref SNPs for V =  80"
[1] "Number cDenovo iSNPs for V =  1139"
[[1]]

[[2]]

[[3]]

[[4]]

[[5]]

[[6]]

[[7]]

[[8]]

[[9]]

Subject 1079

SNP_analysis_pipeline(subject_id = 1079)

[1] "SUBJECT_ID is 1079"
[1] "Rare iSNP cutoff =  3"
[1] "num rare iSNPs =  4383"
[1] "num common iSNPs =  4970"
[1] "Recombination block cutoff = 3"
[1] "Num bases in C recomb blocks=  25694"
[1] "Num bases in R recomb = blocks 19690"
[1] "Num bases in V recomb = blocks 12657"
[1] "Coverage cutoff =  10"
[1] "Numbers of R bases above cutoff is  1018215"
[1] "Numbers of C bases above cutoff is  1036824"
[1] "Numbers of V bases above cutoff is  1035527"
[1] "Number of iSNP positions =  5450"
[1] "R only fixed SNPs (RonlyF) =  0"
[1] "R only rare fixed SNPs (RonlyFrare) =  0"
[1] "R only fixed SNPs in recombinant regions (RonlyFrecomb) =  0"
[1] "R only iSNPs (RonlyRI) =  299"
[1] "R only rare iSNPs (RonlyRIrare) =  137"
[1] "R only iSNPs in recombinant regions (RonlyRIrecomb) =  5"
[1] "C only fixed SNPs (ConlyF) =  0"
[1] "C only rare fixed SNPs (ConlyFrare) =  0"
[1] "C only fixed SNPs in recombinant regions (ConlyFrecomb) =  0"
[1] "C only iSNPs (ConlyRI) =  2"
[1] "C only rare iSNPs (ConlyRIrare) =  0"
[1] "C only iSNPs in recombinant regions (ConlyRIrecomb) =  0"
[1] "V only fixed SNPs (VonlyF) =  0"
[1] "V only rare fixed SNPs (VonlyFrare) =  0"
[1] "V only fixed SNPs in recombinant regions (VonlyFrecombb) =  0"
[1] "V only iSNPs (VonlyRI) =  22"
[1] "V only rare iSNPs (VonlyRIrare) =  8"
[1] "V only iSNPs in recombinant regions (VonlyRIrecomb) =  1"
[1] "RC only fixed SNPs (RConlyF) =  0"
[1] "RC only rare fixed SNPs (RConlyFrare) =  0"
[1] "RC only fixed SNPs in recombinant regions (RConlyFrecomb) =  0"
[1] "RC only iSNPs (RConlyRI) =  2"
[1] "RC only rare iSNPs (RConlyRIrare) =  0"
[1] "RC only iSNPs in recombinant regions (RConlyRIrecomb) =  1"
[1] "RV only fixed SNPs (RVonlyF) =  0"
[1] "RV only rare fixed SNPs (RVonlyFrare) =  0"
[1] "RV only fixed SNPs in recombinant regions (RVonlyFrecomb) =  0"
[1] "RV only iSNPs (RVonlyRI) =  19"
[1] "RV only rare iSNPs (RVonlyRIrare) =  1"
[1] "RV only iSNPs in recombinant regions (RVonlyRIrecomb) =  0"
[1] "VC only fixed SNPs (VConlyF) =  0"
[1] "VC only rare fixed SNPs (VConlyFrare) =  0"
[1] "VC only fixed SNPs in recombinant regions (VConlyFrecomb) =  0"
[1] "VC only iSNPs (VConlyRI) =  1"
[1] "VC only rare iSNPs (VConlyRIrare) =  0"
[1] "VC only iSNPs in recombinant regions (VConlyRIrecomb) =  0"
[1] "All fixed SNPs (AllF) =  2169"
[1] "All rare fixed SNPs (AllFrare) =  858"
[1] "All fixed SNPs in recombinant regions (AllFrecomb) =  197"
[1] "All iSNPs (AllRI) =  7"
[1] "All rare  iSNPs (AllRIrare) =  0"
[1] "All iSNPs in recombinant regions (AllRIrecomb) =  0"
[1] "R is fixed, V only is intermediate, and rare (RonlyF_VIrare) =  0"
[1] "R is fixed, C only is intermediate, and rare (RonlyF_CIrare) =  0"
[1] "R is fixed, V and C are intermediate, and rare (RonlyF_CandVIrare) =  0"
[1] "C is fixed, V only is intermediate, and rare (ConlyF_VIrare) =  0"
[1] "C is fixed, R only is intermediate, and rare (ConlyF_RIrare) =  0"
[1] "C is fixed, R and V are intermediate, and rare (ConlyF_RandVIrare) =  10"
[1] "V is fixed, C only is intermediate, and rare (VonlyF_CIrare) =  0"
[1] "V is fixed, R only is intermediate, and rare (VonlyF_RIrare) =  0"
[1] "V is fixed, R and C are intermediate, and rare (VonlyF_CandRIrare) =  0"
[1] "R and C are fixed, V is intermediate, and rare (RCF_VIrare) =  13"
[1] "R and V are fixed, C is intermediate, and rare (RVF_CIrare) =  0"
[1] "V and C are fixed, R is intermediate, and rare (CVF_RIrare) =  132"

Warning: Removed 3 rows containing missing values (geom_point).
Warning: Removed 46 rows containing missing values (geom_point).
Warning: Removed 4 rows containing missing values (geom_point).
Warning: Removed 53 rows containing non-finite values (stat_boxplot).

[1] "Number cDenovo Ref SNPs for C =  336"
[1] "Number cDenovo Non-Ref SNPs for C =  1532"
[1] "Number cDenovo iSNPs for C =  0"
[1] "Number cDenovo Ref SNPs for R =  244"
[1] "Number cDenovo Non-Ref SNPs for R =  714"
[1] "Number cDenovo iSNPs for R =  867"
[1] "Number cDenovo Ref SNPs for V =  322"
[1] "Number cDenovo Non-Ref SNPs for V =  1393"
[1] "Number cDenovo iSNPs for V =  152"
[[1]]

[[2]]

[[3]]

[[4]]

[[5]]

[[6]]

[[7]]

[[8]]

[[9]]

Subject 1106

SNP_analysis_pipeline(subject_id = 1106)

[1] "SUBJECT_ID is 1106"
[1] "Rare iSNP cutoff =  3"
[1] "num rare iSNPs =  4383"
[1] "num common iSNPs =  4970"
[1] "Recombination block cutoff = 3"
[1] "Num bases in C recomb blocks=  26943"
[1] "Num bases in R recomb = blocks 26722"
[1] "Num bases in V recomb = blocks 3510"
[1] "Coverage cutoff =  10"
[1] "Numbers of R bases above cutoff is  1024517"
[1] "Numbers of C bases above cutoff is  1032626"
[1] "Numbers of V bases above cutoff is  1038242"
[1] "Number of iSNP positions =  692"
[1] "R only fixed SNPs (RonlyF) =  0"
[1] "R only rare fixed SNPs (RonlyFrare) =  0"
[1] "R only fixed SNPs in recombinant regions (RonlyFrecomb) =  0"
[1] "R only iSNPs (RonlyRI) =  0"
[1] "R only rare iSNPs (RonlyRIrare) =  0"
[1] "R only iSNPs in recombinant regions (RonlyRIrecomb) =  0"
[1] "C only fixed SNPs (ConlyF) =  0"
[1] "C only rare fixed SNPs (ConlyFrare) =  0"
[1] "C only fixed SNPs in recombinant regions (ConlyFrecomb) =  0"
[1] "C only iSNPs (ConlyRI) =  0"
[1] "C only rare iSNPs (ConlyRIrare) =  0"
[1] "C only iSNPs in recombinant regions (ConlyRIrecomb) =  0"
[1] "V only fixed SNPs (VonlyF) =  0"
[1] "V only rare fixed SNPs (VonlyFrare) =  0"
[1] "V only fixed SNPs in recombinant regions (VonlyFrecombb) =  0"
[1] "V only iSNPs (VonlyRI) =  1"
[1] "V only rare iSNPs (VonlyRIrare) =  1"
[1] "V only iSNPs in recombinant regions (VonlyRIrecomb) =  1"
[1] "RC only fixed SNPs (RConlyF) =  0"
[1] "RC only rare fixed SNPs (RConlyFrare) =  0"
[1] "RC only fixed SNPs in recombinant regions (RConlyFrecomb) =  0"
[1] "RC only iSNPs (RConlyRI) =  1"
[1] "RC only rare iSNPs (RConlyRIrare) =  0"
[1] "RC only iSNPs in recombinant regions (RConlyRIrecomb) =  1"
[1] "RV only fixed SNPs (RVonlyF) =  0"
[1] "RV only rare fixed SNPs (RVonlyFrare) =  0"
[1] "RV only fixed SNPs in recombinant regions (RVonlyFrecomb) =  0"
[1] "RV only iSNPs (RVonlyRI) =  0"
[1] "RV only rare iSNPs (RVonlyRIrare) =  0"
[1] "RV only iSNPs in recombinant regions (RVonlyRIrecomb) =  0"
[1] "VC only fixed SNPs (VConlyF) =  0"
[1] "VC only rare fixed SNPs (VConlyFrare) =  0"
[1] "VC only fixed SNPs in recombinant regions (VConlyFrecomb) =  0"
[1] "VC only iSNPs (VConlyRI) =  0"
[1] "VC only rare iSNPs (VConlyRIrare) =  0"
[1] "VC only iSNPs in recombinant regions (VConlyRIrecomb) =  0"
[1] "All fixed SNPs (AllF) =  667"
[1] "All rare fixed SNPs (AllFrare) =  425"
[1] "All fixed SNPs in recombinant regions (AllFrecomb) =  137"
[1] "All iSNPs (AllRI) =  6"
[1] "All rare  iSNPs (AllRIrare) =  0"
[1] "All iSNPs in recombinant regions (AllRIrecomb) =  1"
[1] "R is fixed, V only is intermediate, and rare (RonlyF_VIrare) =  0"
[1] "R is fixed, C only is intermediate, and rare (RonlyF_CIrare) =  0"
[1] "R is fixed, V and C are intermediate, and rare (RonlyF_CandVIrare) =  0"
[1] "C is fixed, V only is intermediate, and rare (ConlyF_VIrare) =  0"
[1] "C is fixed, R only is intermediate, and rare (ConlyF_RIrare) =  0"
[1] "C is fixed, R and V are intermediate, and rare (ConlyF_RandVIrare) =  0"
[1] "V is fixed, C only is intermediate, and rare (VonlyF_CIrare) =  0"
[1] "V is fixed, R only is intermediate, and rare (VonlyF_RIrare) =  0"
[1] "V is fixed, R and C are intermediate, and rare (VonlyF_CandRIrare) =  0"
[1] "R and C are fixed, V is intermediate, and rare (RCF_VIrare) =  7"
[1] "R and V are fixed, C is intermediate, and rare (RVF_CIrare) =  0"
[1] "V and C are fixed, R is intermediate, and rare (CVF_RIrare) =  0"

Warning: Removed 21 rows containing missing values (geom_point).
Warning: Removed 42 rows containing missing values (geom_point).
Warning: Removed 7 rows containing missing values (geom_point).
Warning: Removed 70 rows containing non-finite values (stat_boxplot).

[1] "Number cDenovo Ref SNPs for C =  1701"
[1] "Number cDenovo Non-Ref SNPs for C =  149"
[1] "Number cDenovo iSNPs for C =  0"
[1] "Number cDenovo Ref SNPs for R =  1682"
[1] "Number cDenovo Non-Ref SNPs for R =  147"
[1] "Number cDenovo iSNPs for R =  0"
[1] "Number cDenovo Ref SNPs for V =  1711"
[1] "Number cDenovo Non-Ref SNPs for V =  153"
[1] "Number cDenovo iSNPs for V =  0"
[[1]]

[[2]]

[[3]]

[[4]]

[[5]]

[[6]]

[[7]]

[[8]]

[[9]]

Subject 1145

SNP_analysis_pipeline(subject_id = 1145)

[1] "SUBJECT_ID is 1145"
[1] "Rare iSNP cutoff =  3"
[1] "num rare iSNPs =  4383"
[1] "num common iSNPs =  4970"
[1] "Recombination block cutoff = 3"
[1] "Num bases in C recomb blocks=  497"
[1] "Num bases in R recomb = blocks 261"
[1] "Num bases in V recomb = blocks 177"
[1] "Coverage cutoff =  10"
[1] "Numbers of R bases above cutoff is  1026277"
[1] "Numbers of C bases above cutoff is  1034922"
[1] "Numbers of V bases above cutoff is  888302"
[1] "Number of iSNP positions =  4468"
[1] "R only fixed SNPs (RonlyF) =  1"
[1] "R only rare fixed SNPs (RonlyFrare) =  1"
[1] "R only fixed SNPs in recombinant regions (RonlyFrecomb) =  0"
[1] "R only iSNPs (RonlyRI) =  3"
[1] "R only rare iSNPs (RonlyRIrare) =  2"
[1] "R only iSNPs in recombinant regions (RonlyRIrecomb) =  0"
[1] "C only fixed SNPs (ConlyF) =  0"
[1] "C only rare fixed SNPs (ConlyFrare) =  0"
[1] "C only fixed SNPs in recombinant regions (ConlyFrecomb) =  0"
[1] "C only iSNPs (ConlyRI) =  1"
[1] "C only rare iSNPs (ConlyRIrare) =  1"
[1] "C only iSNPs in recombinant regions (ConlyRIrecomb) =  0"
[1] "V only fixed SNPs (VonlyF) =  0"
[1] "V only rare fixed SNPs (VonlyFrare) =  0"
[1] "V only fixed SNPs in recombinant regions (VonlyFrecombb) =  0"
[1] "V only iSNPs (VonlyRI) =  139"
[1] "V only rare iSNPs (VonlyRIrare) =  116"
[1] "V only iSNPs in recombinant regions (VonlyRIrecomb) =  0"
[1] "RC only fixed SNPs (RConlyF) =  0"
[1] "RC only rare fixed SNPs (RConlyFrare) =  0"
[1] "RC only fixed SNPs in recombinant regions (RConlyFrecomb) =  0"
[1] "RC only iSNPs (RConlyRI) =  2"
[1] "RC only rare iSNPs (RConlyRIrare) =  0"
[1] "RC only iSNPs in recombinant regions (RConlyRIrecomb) =  0"
[1] "RV only fixed SNPs (RVonlyF) =  0"
[1] "RV only rare fixed SNPs (RVonlyFrare) =  0"
[1] "RV only fixed SNPs in recombinant regions (RVonlyFrecomb) =  0"
[1] "RV only iSNPs (RVonlyRI) =  1"
[1] "RV only rare iSNPs (RVonlyRIrare) =  0"
[1] "RV only iSNPs in recombinant regions (RVonlyRIrecomb) =  0"
[1] "VC only fixed SNPs (VConlyF) =  0"
[1] "VC only rare fixed SNPs (VConlyFrare) =  0"
[1] "VC only fixed SNPs in recombinant regions (VConlyFrecomb) =  0"
[1] "VC only iSNPs (VConlyRI) =  0"
[1] "VC only rare iSNPs (VConlyRIrare) =  0"
[1] "VC only iSNPs in recombinant regions (VConlyRIrecomb) =  0"
[1] "All fixed SNPs (AllF) =  4155"
[1] "All rare fixed SNPs (AllFrare) =  780"
[1] "All fixed SNPs in recombinant regions (AllFrecomb) =  20"
[1] "All iSNPs (AllRI) =  7"
[1] "All rare  iSNPs (AllRIrare) =  0"
[1] "All iSNPs in recombinant regions (AllRIrecomb) =  0"
[1] "R is fixed, V only is intermediate, and rare (RonlyF_VIrare) =  0"
[1] "R is fixed, C only is intermediate, and rare (RonlyF_CIrare) =  0"
[1] "R is fixed, V and C are intermediate, and rare (RonlyF_CandVIrare) =  0"
[1] "C is fixed, V only is intermediate, and rare (ConlyF_VIrare) =  0"
[1] "C is fixed, R only is intermediate, and rare (ConlyF_RIrare) =  0"
[1] "C is fixed, R and V are intermediate, and rare (ConlyF_RandVIrare) =  0"
[1] "V is fixed, C only is intermediate, and rare (VonlyF_CIrare) =  0"
[1] "V is fixed, R only is intermediate, and rare (VonlyF_RIrare) =  0"
[1] "V is fixed, R and C are intermediate, and rare (VonlyF_CandRIrare) =  0"
[1] "R and C are fixed, V is intermediate, and rare (RCF_VIrare) =  8"
[1] "R and V are fixed, C is intermediate, and rare (RVF_CIrare) =  0"
[1] "V and C are fixed, R is intermediate, and rare (CVF_RIrare) =  0"

Warning: Removed 4 rows containing missing values (geom_point).
Warning: Removed 29 rows containing missing values (geom_point).
Warning: Removed 284 rows containing missing values (geom_point).
Warning: Removed 317 rows containing non-finite values (stat_boxplot).

[1] "Number cDenovo Ref SNPs for C =  336"
[1] "Number cDenovo Non-Ref SNPs for C =  1529"
[1] "Number cDenovo iSNPs for C =  0"
[1] "Number cDenovo Ref SNPs for R =  328"
[1] "Number cDenovo Non-Ref SNPs for R =  1512"
[1] "Number cDenovo iSNPs for R =  0"
[1] "Number cDenovo Ref SNPs for V =  281"
[1] "Number cDenovo Non-Ref SNPs for V =  1265"
[1] "Number cDenovo iSNPs for V =  39"
[[1]]

[[2]]

[[3]]

[[4]]

[[5]]

[[6]]

[[7]]

[[8]]

[[9]]

Subject 1176

SNP_analysis_pipeline(subject_id = 1176)

[1] "SUBJECT_ID is 1176"
[1] "Rare iSNP cutoff =  3"
[1] "num rare iSNPs =  4383"
[1] "num common iSNPs =  4970"
[1] "Recombination block cutoff = 3"
[1] "Num bases in C recomb blocks=  51945"
[1] "Num bases in R recomb = blocks 14626"
[1] "Num bases in V recomb = blocks 13428"
[1] "Coverage cutoff =  10"
[1] "Numbers of R bases above cutoff is  1038149"
[1] "Numbers of C bases above cutoff is  1035843"
[1] "Numbers of V bases above cutoff is  1027021"
[1] "Number of iSNP positions =  6142"
[1] "R only fixed SNPs (RonlyF) =  0"
[1] "R only rare fixed SNPs (RonlyFrare) =  0"
[1] "R only fixed SNPs in recombinant regions (RonlyFrecomb) =  0"
[1] "R only iSNPs (RonlyRI) =  62"
[1] "R only rare iSNPs (RonlyRIrare) =  29"
[1] "R only iSNPs in recombinant regions (RonlyRIrecomb) =  42"
[1] "C only fixed SNPs (ConlyF) =  0"
[1] "C only rare fixed SNPs (ConlyFrare) =  0"
[1] "C only fixed SNPs in recombinant regions (ConlyFrecomb) =  0"
[1] "C only iSNPs (ConlyRI) =  6"
[1] "C only rare iSNPs (ConlyRIrare) =  2"
[1] "C only iSNPs in recombinant regions (ConlyRIrecomb) =  1"
[1] "V only fixed SNPs (VonlyF) =  1"
[1] "V only rare fixed SNPs (VonlyFrare) =  1"
[1] "V only fixed SNPs in recombinant regions (VonlyFrecombb) =  0"
[1] "V only iSNPs (VonlyRI) =  528"
[1] "V only rare iSNPs (VonlyRIrare) =  303"
[1] "V only iSNPs in recombinant regions (VonlyRIrecomb) =  54"
[1] "RC only fixed SNPs (RConlyF) =  53"
[1] "RC only rare fixed SNPs (RConlyFrare) =  25"
[1] "RC only fixed SNPs in recombinant regions (RConlyFrecomb) =  0"
[1] "RC only iSNPs (RConlyRI) =  330"
[1] "RC only rare iSNPs (RConlyRIrare) =  90"
[1] "RC only iSNPs in recombinant regions (RConlyRIrecomb) =  195"
[1] "RV only fixed SNPs (RVonlyF) =  0"
[1] "RV only rare fixed SNPs (RVonlyFrare) =  0"
[1] "RV only fixed SNPs in recombinant regions (RVonlyFrecomb) =  0"
[1] "RV only iSNPs (RVonlyRI) =  18"
[1] "RV only rare iSNPs (RVonlyRIrare) =  5"
[1] "RV only iSNPs in recombinant regions (RVonlyRIrecomb) =  8"
[1] "VC only fixed SNPs (VConlyF) =  0"
[1] "VC only rare fixed SNPs (VConlyFrare) =  0"
[1] "VC only fixed SNPs in recombinant regions (VConlyFrecomb) =  0"
[1] "VC only iSNPs (VConlyRI) =  0"
[1] "VC only rare iSNPs (VConlyRIrare) =  0"
[1] "VC only iSNPs in recombinant regions (VConlyRIrecomb) =  0"
[1] "All fixed SNPs (AllF) =  380"
[1] "All rare fixed SNPs (AllFrare) =  372"
[1] "All fixed SNPs in recombinant regions (AllFrecomb) =  47"
[1] "All iSNPs (AllRI) =  322"
[1] "All rare  iSNPs (AllRIrare) =  88"
[1] "All iSNPs in recombinant regions (AllRIrecomb) =  86"
[1] "R is fixed, V only is intermediate, and rare (RonlyF_VIrare) =  0"
[1] "R is fixed, C only is intermediate, and rare (RonlyF_CIrare) =  0"
[1] "R is fixed, V and C are intermediate, and rare (RonlyF_CandVIrare) =  0"
[1] "C is fixed, V only is intermediate, and rare (ConlyF_VIrare) =  0"
[1] "C is fixed, R only is intermediate, and rare (ConlyF_RIrare) =  7"
[1] "C is fixed, R and V are intermediate, and rare (ConlyF_RandVIrare) =  7"
[1] "V is fixed, C only is intermediate, and rare (VonlyF_CIrare) =  0"
[1] "V is fixed, R only is intermediate, and rare (VonlyF_RIrare) =  0"
[1] "V is fixed, R and C are intermediate, and rare (VonlyF_CandRIrare) =  41"
[1] "R and C are fixed, V is intermediate, and rare (RCF_VIrare) =  504"
[1] "R and V are fixed, C is intermediate, and rare (RVF_CIrare) =  0"
[1] "V and C are fixed, R is intermediate, and rare (CVF_RIrare) =  59"

Warning: Removed 4 rows containing missing values (geom_point).
Warning: Removed 1 rows containing missing values (geom_point).
Warning: Removed 21 rows containing missing values (geom_point).
Warning: Removed 26 rows containing non-finite values (stat_boxplot).

[1] "Number cDenovo Ref SNPs for C =  335"
[1] "Number cDenovo Non-Ref SNPs for C =  1517"
[1] "Number cDenovo iSNPs for C =  16"
[1] "Number cDenovo Ref SNPs for R =  333"
[1] "Number cDenovo Non-Ref SNPs for R =  1373"
[1] "Number cDenovo iSNPs for R =  165"
[1] "Number cDenovo Ref SNPs for V =  189"
[1] "Number cDenovo Non-Ref SNPs for V =  94"
[1] "Number cDenovo iSNPs for V =  1568"
[[1]]

[[2]]

[[3]]

[[4]]

[[5]]

[[6]]

[[7]]

[[8]]

[[9]]

Subject 1182

SNP_analysis_pipeline(subject_id = 1182)

[1] "SUBJECT_ID is 1182"
[1] "Rare iSNP cutoff =  3"
[1] "num rare iSNPs =  4383"
[1] "num common iSNPs =  4970"
[1] "Recombination block cutoff = 3"
[1] "Num bases in C recomb blocks=  1474"
[1] "Num bases in R recomb = blocks 3396"
[1] "Num bases in V recomb = blocks 24510"
[1] "Coverage cutoff =  10"
[1] "Numbers of R bases above cutoff is  1036038"
[1] "Numbers of C bases above cutoff is  1029053"
[1] "Numbers of V bases above cutoff is  1035249"
[1] "Number of iSNP positions =  5725"
[1] "R only fixed SNPs (RonlyF) =  20"
[1] "R only rare fixed SNPs (RonlyFrare) =  13"
[1] "R only fixed SNPs in recombinant regions (RonlyFrecomb) =  0"
[1] "R only iSNPs (RonlyRI) =  361"
[1] "R only rare iSNPs (RonlyRIrare) =  165"
[1] "R only iSNPs in recombinant regions (RonlyRIrecomb) =  33"
[1] "C only fixed SNPs (ConlyF) =  0"
[1] "C only rare fixed SNPs (ConlyFrare) =  0"
[1] "C only fixed SNPs in recombinant regions (ConlyFrecomb) =  0"
[1] "C only iSNPs (ConlyRI) =  10"
[1] "C only rare iSNPs (ConlyRIrare) =  7"
[1] "C only iSNPs in recombinant regions (ConlyRIrecomb) =  1"
[1] "V only fixed SNPs (VonlyF) =  0"
[1] "V only rare fixed SNPs (VonlyFrare) =  0"
[1] "V only fixed SNPs in recombinant regions (VonlyFrecombb) =  0"
[1] "V only iSNPs (VonlyRI) =  2"
[1] "V only rare iSNPs (VonlyRIrare) =  2"
[1] "V only iSNPs in recombinant regions (VonlyRIrecomb) =  0"
[1] "RC only fixed SNPs (RConlyF) =  0"
[1] "RC only rare fixed SNPs (RConlyFrare) =  0"
[1] "RC only fixed SNPs in recombinant regions (RConlyFrecomb) =  0"
[1] "RC only iSNPs (RConlyRI) =  0"
[1] "RC only rare iSNPs (RConlyRIrare) =  0"
[1] "RC only iSNPs in recombinant regions (RConlyRIrecomb) =  0"
[1] "RV only fixed SNPs (RVonlyF) =  0"
[1] "RV only rare fixed SNPs (RVonlyFrare) =  0"
[1] "RV only fixed SNPs in recombinant regions (RVonlyFrecomb) =  0"
[1] "RV only iSNPs (RVonlyRI) =  19"
[1] "RV only rare iSNPs (RVonlyRIrare) =  8"
[1] "RV only iSNPs in recombinant regions (RVonlyRIrecomb) =  3"
[1] "VC only fixed SNPs (VConlyF) =  470"
[1] "VC only rare fixed SNPs (VConlyFrare) =  207"
[1] "VC only fixed SNPs in recombinant regions (VConlyFrecomb) =  36"
[1] "VC only iSNPs (VConlyRI) =  27"
[1] "VC only rare iSNPs (VConlyRIrare) =  0"
[1] "VC only iSNPs in recombinant regions (VConlyRIrecomb) =  10"
[1] "All fixed SNPs (AllF) =  241"
[1] "All rare fixed SNPs (AllFrare) =  218"
[1] "All fixed SNPs in recombinant regions (AllFrecomb) =  50"
[1] "All iSNPs (AllRI) =  3"
[1] "All rare  iSNPs (AllRIrare) =  0"
[1] "All iSNPs in recombinant regions (AllRIrecomb) =  0"
[1] "R is fixed, V only is intermediate, and rare (RonlyF_VIrare) =  0"
[1] "R is fixed, C only is intermediate, and rare (RonlyF_CIrare) =  0"
[1] "R is fixed, V and C are intermediate, and rare (RonlyF_CandVIrare) =  0"
[1] "C is fixed, V only is intermediate, and rare (ConlyF_VIrare) =  91"
[1] "C is fixed, R only is intermediate, and rare (ConlyF_RIrare) =  0"
[1] "C is fixed, R and V are intermediate, and rare (ConlyF_RandVIrare) =  31"
[1] "V is fixed, C only is intermediate, and rare (VonlyF_CIrare) =  0"
[1] "V is fixed, R only is intermediate, and rare (VonlyF_RIrare) =  0"
[1] "V is fixed, R and C are intermediate, and rare (VonlyF_CandRIrare) =  0"
[1] "R and C are fixed, V is intermediate, and rare (RCF_VIrare) =  0"
[1] "R and V are fixed, C is intermediate, and rare (RVF_CIrare) =  0"
[1] "V and C are fixed, R is intermediate, and rare (CVF_RIrare) =  508"

Warning: Removed 29 rows containing missing values (geom_point).
Warning: Removed 1 rows containing missing values (geom_point).
Warning: Removed 16 rows containing missing values (geom_point).
Warning: Removed 46 rows containing non-finite values (stat_boxplot).

[1] "Number cDenovo Ref SNPs for C =  334"
[1] "Number cDenovo Non-Ref SNPs for C =  1509"
[1] "Number cDenovo iSNPs for C =  0"
[1] "Number cDenovo Ref SNPs for R =  370"
[1] "Number cDenovo Non-Ref SNPs for R =  59"
[1] "Number cDenovo iSNPs for R =  1442"
[1] "Number cDenovo Ref SNPs for V =  331"
[1] "Number cDenovo Non-Ref SNPs for V =  1358"
[1] "Number cDenovo iSNPs for V =  167"
[[1]]

[[2]]

[[3]]

[[4]]

[[5]]

[[6]]

[[7]]

[[8]]

[[9]]

Subject 1201

SNP_analysis_pipeline(subject_id = 1201)

[1] "SUBJECT_ID is 1201"
[1] "Rare iSNP cutoff =  3"
[1] "num rare iSNPs =  4383"
[1] "num common iSNPs =  4970"
[1] "Recombination block cutoff = 3"
[1] "Num bases in C recomb blocks=  803"
[1] "Num bases in R recomb = blocks 184"
[1] "Num bases in V recomb = blocks 670"
[1] "Coverage cutoff =  10"
[1] "Numbers of R bases above cutoff is  1038120"
[1] "Numbers of C bases above cutoff is  1025145"
[1] "Numbers of V bases above cutoff is  1037114"
[1] "Number of iSNP positions =  1147"
[1] "R only fixed SNPs (RonlyF) =  1"
[1] "R only rare fixed SNPs (RonlyFrare) =  1"
[1] "R only fixed SNPs in recombinant regions (RonlyFrecomb) =  0"
[1] "R only iSNPs (RonlyRI) =  11"
[1] "R only rare iSNPs (RonlyRIrare) =  2"
[1] "R only iSNPs in recombinant regions (RonlyRIrecomb) =  0"
[1] "C only fixed SNPs (ConlyF) =  0"
[1] "C only rare fixed SNPs (ConlyFrare) =  0"
[1] "C only fixed SNPs in recombinant regions (ConlyFrecomb) =  0"
[1] "C only iSNPs (ConlyRI) =  0"
[1] "C only rare iSNPs (ConlyRIrare) =  0"
[1] "C only iSNPs in recombinant regions (ConlyRIrecomb) =  0"
[1] "V only fixed SNPs (VonlyF) =  0"
[1] "V only rare fixed SNPs (VonlyFrare) =  0"
[1] "V only fixed SNPs in recombinant regions (VonlyFrecombb) =  0"
[1] "V only iSNPs (VonlyRI) =  0"
[1] "V only rare iSNPs (VonlyRIrare) =  0"
[1] "V only iSNPs in recombinant regions (VonlyRIrecomb) =  0"
[1] "RC only fixed SNPs (RConlyF) =  0"
[1] "RC only rare fixed SNPs (RConlyFrare) =  0"
[1] "RC only fixed SNPs in recombinant regions (RConlyFrecomb) =  0"
[1] "RC only iSNPs (RConlyRI) =  0"
[1] "RC only rare iSNPs (RConlyRIrare) =  0"
[1] "RC only iSNPs in recombinant regions (RConlyRIrecomb) =  0"
[1] "RV only fixed SNPs (RVonlyF) =  0"
[1] "RV only rare fixed SNPs (RVonlyFrare) =  0"
[1] "RV only fixed SNPs in recombinant regions (RVonlyFrecomb) =  0"
[1] "RV only iSNPs (RVonlyRI) =  0"
[1] "RV only rare iSNPs (RVonlyRIrare) =  0"
[1] "RV only iSNPs in recombinant regions (RVonlyRIrecomb) =  0"
[1] "VC only fixed SNPs (VConlyF) =  0"
[1] "VC only rare fixed SNPs (VConlyFrare) =  0"
[1] "VC only fixed SNPs in recombinant regions (VConlyFrecomb) =  0"
[1] "VC only iSNPs (VConlyRI) =  2"
[1] "VC only rare iSNPs (VConlyRIrare) =  1"
[1] "VC only iSNPs in recombinant regions (VConlyRIrecomb) =  0"
[1] "All fixed SNPs (AllF) =  1086"
[1] "All rare fixed SNPs (AllFrare) =  729"
[1] "All fixed SNPs in recombinant regions (AllFrecomb) =  14"
[1] "All iSNPs (AllRI) =  10"
[1] "All rare  iSNPs (AllRIrare) =  0"
[1] "All iSNPs in recombinant regions (AllRIrecomb) =  0"
[1] "R is fixed, V only is intermediate, and rare (RonlyF_VIrare) =  0"
[1] "R is fixed, C only is intermediate, and rare (RonlyF_CIrare) =  0"
[1] "R is fixed, V and C are intermediate, and rare (RonlyF_CandVIrare) =  0"
[1] "C is fixed, V only is intermediate, and rare (ConlyF_VIrare) =  0"
[1] "C is fixed, R only is intermediate, and rare (ConlyF_RIrare) =  0"
[1] "C is fixed, R and V are intermediate, and rare (ConlyF_RandVIrare) =  0"
[1] "V is fixed, C only is intermediate, and rare (VonlyF_CIrare) =  0"
[1] "V is fixed, R only is intermediate, and rare (VonlyF_RIrare) =  0"
[1] "V is fixed, R and C are intermediate, and rare (VonlyF_CandRIrare) =  0"
[1] "R and C are fixed, V is intermediate, and rare (RCF_VIrare) =  0"
[1] "R and V are fixed, C is intermediate, and rare (RVF_CIrare) =  0"
[1] "V and C are fixed, R is intermediate, and rare (CVF_RIrare) =  18"

Warning: Removed 36 rows containing missing values (geom_point).
Warning: Removed 1 rows containing missing values (geom_point).
Warning: Removed 7 rows containing missing values (geom_point).
Warning: Removed 44 rows containing non-finite values (stat_boxplot).

[1] "Number cDenovo Ref SNPs for C =  1597"
[1] "Number cDenovo Non-Ref SNPs for C =  237"
[1] "Number cDenovo iSNPs for C =  0"
[1] "Number cDenovo Ref SNPs for R =  1621"
[1] "Number cDenovo Non-Ref SNPs for R =  246"
[1] "Number cDenovo iSNPs for R =  2"
[1] "Number cDenovo Ref SNPs for V =  1617"
[1] "Number cDenovo Non-Ref SNPs for V =  246"
[1] "Number cDenovo iSNPs for V =  0"
[[1]]

[[2]]

[[3]]

[[4]]

[[5]]

[[6]]

[[7]]

[[8]]

[[9]]

Subject 1226

SNP_analysis_pipeline(subject_id = 1226)

[1] "SUBJECT_ID is 1226"
[1] "Rare iSNP cutoff =  3"
[1] "num rare iSNPs =  4383"
[1] "num common iSNPs =  4970"
[1] "Recombination block cutoff = 3"
[1] "Num bases in C recomb blocks=  4431"
[1] "Num bases in R recomb = blocks 4431"
[1] "Num bases in V recomb = blocks 4431"
[1] "Coverage cutoff =  10"
[1] "Numbers of R bases above cutoff is  1018587"
[1] "Numbers of C bases above cutoff is  1035547"
[1] "Numbers of V bases above cutoff is  1033213"
[1] "Number of iSNP positions =  5206"
[1] "R only fixed SNPs (RonlyF) =  1"
[1] "R only rare fixed SNPs (RonlyFrare) =  1"
[1] "R only fixed SNPs in recombinant regions (RonlyFrecomb) =  0"
[1] "R only iSNPs (RonlyRI) =  26"
[1] "R only rare iSNPs (RonlyRIrare) =  22"
[1] "R only iSNPs in recombinant regions (RonlyRIrecomb) =  0"
[1] "C only fixed SNPs (ConlyF) =  0"
[1] "C only rare fixed SNPs (ConlyFrare) =  0"
[1] "C only fixed SNPs in recombinant regions (ConlyFrecomb) =  0"
[1] "C only iSNPs (ConlyRI) =  2"
[1] "C only rare iSNPs (ConlyRIrare) =  2"
[1] "C only iSNPs in recombinant regions (ConlyRIrecomb) =  0"
[1] "V only fixed SNPs (VonlyF) =  0"
[1] "V only rare fixed SNPs (VonlyFrare) =  0"
[1] "V only fixed SNPs in recombinant regions (VonlyFrecombb) =  0"
[1] "V only iSNPs (VonlyRI) =  2"
[1] "V only rare iSNPs (VonlyRIrare) =  2"
[1] "V only iSNPs in recombinant regions (VonlyRIrecomb) =  0"
[1] "RC only fixed SNPs (RConlyF) =  0"
[1] "RC only rare fixed SNPs (RConlyFrare) =  0"
[1] "RC only fixed SNPs in recombinant regions (RConlyFrecomb) =  0"
[1] "RC only iSNPs (RConlyRI) =  0"
[1] "RC only rare iSNPs (RConlyRIrare) =  0"
[1] "RC only iSNPs in recombinant regions (RConlyRIrecomb) =  0"
[1] "RV only fixed SNPs (RVonlyF) =  0"
[1] "RV only rare fixed SNPs (RVonlyFrare) =  0"
[1] "RV only fixed SNPs in recombinant regions (RVonlyFrecomb) =  0"
[1] "RV only iSNPs (RVonlyRI) =  0"
[1] "RV only rare iSNPs (RVonlyRIrare) =  0"
[1] "RV only iSNPs in recombinant regions (RVonlyRIrecomb) =  0"
[1] "VC only fixed SNPs (VConlyF) =  0"
[1] "VC only rare fixed SNPs (VConlyFrare) =  0"
[1] "VC only fixed SNPs in recombinant regions (VConlyFrecomb) =  0"
[1] "VC only iSNPs (VConlyRI) =  1"
[1] "VC only rare iSNPs (VConlyRIrare) =  0"
[1] "VC only iSNPs in recombinant regions (VConlyRIrecomb) =  0"
[1] "All fixed SNPs (AllF) =  5134"
[1] "All rare fixed SNPs (AllFrare) =  1056"
[1] "All fixed SNPs in recombinant regions (AllFrecomb) =  1"
[1] "All iSNPs (AllRI) =  24"
[1] "All rare  iSNPs (AllRIrare) =  0"
[1] "All iSNPs in recombinant regions (AllRIrecomb) =  0"
[1] "R is fixed, V only is intermediate, and rare (RonlyF_VIrare) =  0"
[1] "R is fixed, C only is intermediate, and rare (RonlyF_CIrare) =  0"
[1] "R is fixed, V and C are intermediate, and rare (RonlyF_CandVIrare) =  0"
[1] "C is fixed, V only is intermediate, and rare (ConlyF_VIrare) =  0"
[1] "C is fixed, R only is intermediate, and rare (ConlyF_RIrare) =  0"
[1] "C is fixed, R and V are intermediate, and rare (ConlyF_RandVIrare) =  0"
[1] "V is fixed, C only is intermediate, and rare (VonlyF_CIrare) =  0"
[1] "V is fixed, R only is intermediate, and rare (VonlyF_RIrare) =  0"
[1] "V is fixed, R and C are intermediate, and rare (VonlyF_CandRIrare) =  0"
[1] "R and C are fixed, V is intermediate, and rare (RCF_VIrare) =  0"
[1] "R and V are fixed, C is intermediate, and rare (RVF_CIrare) =  0"
[1] "V and C are fixed, R is intermediate, and rare (CVF_RIrare) =  0"

Warning: Removed 3 rows containing missing values (geom_point).
Warning: Removed 15 rows containing missing values (geom_point).
Warning: Removed 10 rows containing missing values (geom_point).
Warning: Removed 28 rows containing non-finite values (stat_boxplot).

[1] "Number cDenovo Ref SNPs for C =  342"
[1] "Number cDenovo Non-Ref SNPs for C =  1526"
[1] "Number cDenovo iSNPs for C =  0"
[1] "Number cDenovo Ref SNPs for R =  337"
[1] "Number cDenovo Non-Ref SNPs for R =  1517"
[1] "Number cDenovo iSNPs for R =  2"
[1] "Number cDenovo Ref SNPs for V =  337"
[1] "Number cDenovo Non-Ref SNPs for V =  1524"
[1] "Number cDenovo iSNPs for V =  0"
[[1]]

[[2]]

[[3]]

[[4]]

[[5]]

[[6]]

[[7]]

[[8]]

[[9]]